5BV2 | pdb_00005bv2

Crystal structure of E. coli HPII catalase variant

PDB DOI: https://doi.org/10.2210/pdb5BV2/pdb

Classification: OXIDOREDUCTASE
Organism(s): Escherichia coli
Mutation(s): No

Deposited: 2015-06-04 Released: 2015-06-24
Deposition Author(s): Wang, J., Lomkalin, I.V.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.53 Å
R-Value Free:
0.132 (Depositor), 0.130 (DCC)
R-Value Work:
0.082 (Depositor), 0.080 (DCC)
R-Value Observed:
0.085 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

Literature

Influence of weak-intensity data, ordered water molecules, and hydrogen atoms on the refinement of a large protein crystal structure

Wang, J., Lomkalin, I.V.

To be published.

Macromolecule Content

Total Structure Weight: 344.49 kDa
Atom Count: 29,414
Modeled Residue Count: 2,987
Deposited Residue Count: 3,012
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Catalase HPII	A [auth P], B [auth Q], C [auth R], D [auth S]	753	Escherichia coli	Mutation(s): 0 EC: 1.11.1.6
UniProt
Find proteins for P21179 (Escherichia coli (strain K12)) Explore P21179 Go to UniProtKB: P21179
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P21179
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 8 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HDD Query on HDD Download Ideal Coordinates CCD File SDF format, chain E [auth P] SDF format, chain HB [auth S] SDF format, chain VA [auth R] SDF format, chain W [auth Q] MOL2 format, chain E [auth P] MOL2 format, chain HB [auth S] MOL2 format, chain VA [auth R] MOL2 format, chain W [auth Q] mmCIF format, chain E [auth P] mmCIF format, chain HB [auth S] mmCIF format, chain VA [auth R] mmCIF format, chain W [auth Q]	E [auth P], HB [auth S], VA [auth R], W [auth Q]	CIS-HEME D HYDROXYCHLORIN GAMMA-SPIROLACTONE C₃₄ H₃₂ Fe N₄ O₅ UMGOPAWIGKFTRK-QQDQPIDJSA-N		Interactions Focus chain E [auth P] Focus chain HB [auth S] Focus chain VA [auth R] Focus chain W [auth Q] Interactions & Density Focus chain E [auth P] Focus chain HB [auth S] Focus chain VA [auth R] Focus chain W [auth Q]
PG4 Query on PG4 Download Ideal Coordinates CCD File SDF format, chain GB [auth R] MOL2 format, chain GB [auth R] mmCIF format, chain GB [auth R]	GB [auth R]	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Interactions Focus chain GB [auth R] Interactions & Density Focus chain GB [auth R]
PGE Query on PGE Download Ideal Coordinates CCD File SDF format, chain BB [auth R] SDF format, chain CB [auth R] SDF format, chain P MOL2 format, chain BB [auth R] MOL2 format, chain CB [auth R] MOL2 format, chain P mmCIF format, chain BB [auth R] mmCIF format, chain CB [auth R] mmCIF format, chain P	BB [auth R], CB [auth R], P	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain BB [auth R] Focus chain CB [auth R] Focus chain P Interactions & Density Focus chain BB [auth R] Focus chain CB [auth R] Focus chain P
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain R [auth P] SDF format, chain RA [auth Q] SDF format, chain S [auth P] SDF format, chain SA [auth Q] SDF format, chain T [auth P] SDF format, chain TA [auth Q] SDF format, chain U [auth P] SDF format, chain UA [auth Q] SDF format, chain WB [auth S] SDF format, chain XB [auth S] MOL2 format, chain R [auth P] MOL2 format, chain RA [auth Q] MOL2 format, chain S [auth P] MOL2 format, chain SA [auth Q] MOL2 format, chain T [auth P] MOL2 format, chain TA [auth Q] MOL2 format, chain U [auth P] MOL2 format, chain UA [auth Q] MOL2 format, chain WB [auth S] MOL2 format, chain XB [auth S] mmCIF format, chain R [auth P] mmCIF format, chain RA [auth Q] mmCIF format, chain S [auth P] mmCIF format, chain SA [auth Q] mmCIF format, chain T [auth P] mmCIF format, chain TA [auth Q] mmCIF format, chain U [auth P] mmCIF format, chain UA [auth Q] mmCIF format, chain WB [auth S] mmCIF format, chain XB [auth S]	R [auth P] RA [auth Q] S [auth P] SA [auth Q] T [auth P] R [auth P], RA [auth Q], S [auth P], SA [auth Q], T [auth P], TA [auth Q], U [auth P], UA [auth Q], WB [auth S], XB [auth S]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain R [auth P] Focus chain RA [auth Q] Focus chain S [auth P] Focus chain SA [auth Q] Focus chain T [auth P] Focus chain TA [auth Q] Focus chain U [auth P] Focus chain UA [auth Q] Focus chain WB [auth S] Focus chain XB [auth S] Interactions & Density Focus chain R [auth P] Focus chain RA [auth Q] Focus chain S [auth P] Focus chain SA [auth Q] Focus chain T [auth P] Focus chain TA [auth Q] Focus chain U [auth P] Focus chain UA [auth Q] Focus chain WB [auth S] Focus chain XB [auth S]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain UB [auth S] SDF format, chain V [auth P] MOL2 format, chain UB [auth S] MOL2 format, chain V [auth P] mmCIF format, chain UB [auth S] mmCIF format, chain V [auth P]	UB [auth S], V [auth P]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain UB [auth S] Focus chain V [auth P] Interactions & Density Focus chain UB [auth S] Focus chain V [auth P]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain DB [auth R] SDF format, chain EB [auth R] SDF format, chain F [auth P] SDF format, chain IB [auth S] SDF format, chain PA [auth Q] SDF format, chain Q [auth P] SDF format, chain QA [auth Q] SDF format, chain SB [auth S] SDF format, chain TB [auth S] SDF format, chain WA [auth R] SDF format, chain X [auth Q] MOL2 format, chain DB [auth R] MOL2 format, chain EB [auth R] MOL2 format, chain F [auth P] MOL2 format, chain IB [auth S] MOL2 format, chain PA [auth Q] MOL2 format, chain Q [auth P] MOL2 format, chain QA [auth Q] MOL2 format, chain SB [auth S] MOL2 format, chain TB [auth S] MOL2 format, chain WA [auth R] MOL2 format, chain X [auth Q] mmCIF format, chain DB [auth R] mmCIF format, chain EB [auth R] mmCIF format, chain F [auth P] mmCIF format, chain IB [auth S] mmCIF format, chain PA [auth Q] mmCIF format, chain Q [auth P] mmCIF format, chain QA [auth Q] mmCIF format, chain SB [auth S] mmCIF format, chain TB [auth S] mmCIF format, chain WA [auth R] mmCIF format, chain X [auth Q]	DB [auth R] EB [auth R] F [auth P] IB [auth S] PA [auth Q] DB [auth R], EB [auth R], F [auth P], IB [auth S], PA [auth Q], Q [auth P], QA [auth Q], SB [auth S], TB [auth S], WA [auth R], X [auth Q]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain DB [auth R] Focus chain EB [auth R] Focus chain F [auth P] Focus chain IB [auth S] Focus chain PA [auth Q] Focus chain Q [auth P] Focus chain QA [auth Q] Focus chain SB [auth S] Focus chain TB [auth S] Focus chain WA [auth R] Focus chain X [auth Q] Interactions & Density Focus chain DB [auth R] Focus chain EB [auth R] Focus chain F [auth P] Focus chain IB [auth S] Focus chain PA [auth Q] Focus chain Q [auth P] Focus chain QA [auth Q] Focus chain SB [auth S] Focus chain TB [auth S] Focus chain WA [auth R] Focus chain X [auth Q]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain AA [auth Q] SDF format, chain AB [auth R] SDF format, chain BA [auth Q] SDF format, chain CA [auth Q] SDF format, chain DA [auth Q] SDF format, chain EA [auth Q] SDF format, chain FA [auth Q] SDF format, chain G [auth P] SDF format, chain GA [auth Q] SDF format, chain H [auth P] SDF format, chain HA [auth Q] SDF format, chain I [auth P] SDF format, chain IA [auth Q] SDF format, chain J [auth P] SDF format, chain JA [auth Q] SDF format, chain JB [auth S] SDF format, chain K [auth P] SDF format, chain KA [auth Q] SDF format, chain KB [auth S] SDF format, chain L [auth P] SDF format, chain LA [auth Q] SDF format, chain LB [auth S] SDF format, chain M [auth P] SDF format, chain MA [auth Q] SDF format, chain MB [auth S] SDF format, chain N [auth P] SDF format, chain NA [auth Q] SDF format, chain NB [auth S] SDF format, chain O [auth P] SDF format, chain OA [auth Q] SDF format, chain OB [auth S] SDF format, chain PB [auth S] SDF format, chain QB [auth S] SDF format, chain RB [auth S] SDF format, chain XA [auth R] SDF format, chain Y [auth Q] SDF format, chain YA [auth R] SDF format, chain Z [auth Q] SDF format, chain ZA [auth R] MOL2 format, chain AA [auth Q] MOL2 format, chain AB [auth R] MOL2 format, chain BA [auth Q] MOL2 format, chain CA [auth Q] MOL2 format, chain DA [auth Q] MOL2 format, chain EA [auth Q] MOL2 format, chain FA [auth Q] MOL2 format, chain G [auth P] MOL2 format, chain GA [auth Q] MOL2 format, chain H [auth P] MOL2 format, chain HA [auth Q] MOL2 format, chain I [auth P] MOL2 format, chain IA [auth Q] MOL2 format, chain J [auth P] MOL2 format, chain JA [auth Q] MOL2 format, chain JB [auth S] MOL2 format, chain K [auth P] MOL2 format, chain KA [auth Q] MOL2 format, chain KB [auth S] MOL2 format, chain L [auth P] MOL2 format, chain LA [auth Q] MOL2 format, chain LB [auth S] MOL2 format, chain M [auth P] MOL2 format, chain MA [auth Q] MOL2 format, chain MB [auth S] MOL2 format, chain N [auth P] MOL2 format, chain NA [auth Q] MOL2 format, chain NB [auth S] MOL2 format, chain O [auth P] MOL2 format, chain OA [auth Q] MOL2 format, chain OB [auth S] MOL2 format, chain PB [auth S] MOL2 format, chain QB [auth S] MOL2 format, chain RB [auth S] MOL2 format, chain XA [auth R] MOL2 format, chain Y [auth Q] MOL2 format, chain YA [auth R] MOL2 format, chain Z [auth Q] MOL2 format, chain ZA [auth R] mmCIF format, chain AA [auth Q] mmCIF format, chain AB [auth R] mmCIF format, chain BA [auth Q] mmCIF format, chain CA [auth Q] mmCIF format, chain DA [auth Q] mmCIF format, chain EA [auth Q] mmCIF format, chain FA [auth Q] mmCIF format, chain G [auth P] mmCIF format, chain GA [auth Q] mmCIF format, chain H [auth P] mmCIF format, chain HA [auth Q] mmCIF format, chain I [auth P] mmCIF format, chain IA [auth Q] mmCIF format, chain J [auth P] mmCIF format, chain JA [auth Q] mmCIF format, chain JB [auth S] mmCIF format, chain K [auth P] mmCIF format, chain KA [auth Q] mmCIF format, chain KB [auth S] mmCIF format, chain L [auth P] mmCIF format, chain LA [auth Q] mmCIF format, chain LB [auth S] mmCIF format, chain M [auth P] mmCIF format, chain MA [auth Q] mmCIF format, chain MB [auth S] mmCIF format, chain N [auth P] mmCIF format, chain NA [auth Q] mmCIF format, chain NB [auth S] mmCIF format, chain O [auth P] mmCIF format, chain OA [auth Q] mmCIF format, chain OB [auth S] mmCIF format, chain PB [auth S] mmCIF format, chain QB [auth S] mmCIF format, chain RB [auth S] mmCIF format, chain XA [auth R] mmCIF format, chain Y [auth Q] mmCIF format, chain YA [auth R] mmCIF format, chain Z [auth Q] mmCIF format, chain ZA [auth R]	AA [auth Q] AB [auth R] BA [auth Q] CA [auth Q] DA [auth Q] AA [auth Q], AB [auth R], BA [auth Q], CA [auth Q], DA [auth Q], EA [auth Q], FA [auth Q], G [auth P], GA [auth Q], H [auth P], HA [auth Q], I [auth P], IA [auth Q], J [auth P], JA [auth Q], JB [auth S], K [auth P], KA [auth Q], KB [auth S], L [auth P], LA [auth Q], LB [auth S], M [auth P], MA [auth Q], MB [auth S], N [auth P], NA [auth Q], NB [auth S], O [auth P], OA [auth Q], OB [auth S], PB [auth S], QB [auth S], RB [auth S], XA [auth R], Y [auth Q], YA [auth R], Z [auth Q], ZA [auth R]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain AA [auth Q] Focus chain AB [auth R] Focus chain BA [auth Q] Focus chain CA [auth Q] Focus chain DA [auth Q] Focus chain EA [auth Q] Focus chain FA [auth Q] Focus chain G [auth P] Focus chain GA [auth Q] Focus chain H [auth P] Focus chain HA [auth Q] Focus chain I [auth P] Focus chain IA [auth Q] Focus chain J [auth P] Focus chain JA [auth Q] Focus chain JB [auth S] Focus chain K [auth P] Focus chain KA [auth Q] Focus chain KB [auth S] Focus chain L [auth P] Focus chain LA [auth Q] Focus chain LB [auth S] Focus chain M [auth P] Focus chain MA [auth Q] Focus chain MB [auth S] Focus chain N [auth P] Focus chain NA [auth Q] Focus chain NB [auth S] Focus chain O [auth P] Focus chain OA [auth Q] Focus chain OB [auth S] Focus chain PB [auth S] Focus chain QB [auth S] Focus chain RB [auth S] Focus chain XA [auth R] Focus chain Y [auth Q] Focus chain YA [auth R] Focus chain Z [auth Q] Focus chain ZA [auth R] Interactions & Density Focus chain AA [auth Q] Focus chain AB [auth R] Focus chain BA [auth Q] Focus chain CA [auth Q] Focus chain DA [auth Q] Focus chain EA [auth Q] Focus chain FA [auth Q] Focus chain G [auth P] Focus chain GA [auth Q] Focus chain H [auth P] Focus chain HA [auth Q] Focus chain I [auth P] Focus chain IA [auth Q] Focus chain J [auth P] Focus chain JA [auth Q] Focus chain JB [auth S] Focus chain K [auth P] Focus chain KA [auth Q] Focus chain KB [auth S] Focus chain L [auth P] Focus chain LA [auth Q] Focus chain LB [auth S] Focus chain M [auth P] Focus chain MA [auth Q] Focus chain MB [auth S] Focus chain N [auth P] Focus chain NA [auth Q] Focus chain NB [auth S] Focus chain O [auth P] Focus chain OA [auth Q] Focus chain OB [auth S] Focus chain PB [auth S] Focus chain QB [auth S] Focus chain RB [auth S] Focus chain XA [auth R] Focus chain Y [auth Q] Focus chain YA [auth R] Focus chain Z [auth Q] Focus chain ZA [auth R]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain FB [auth R] SDF format, chain VB [auth S] MOL2 format, chain FB [auth R] MOL2 format, chain VB [auth S] mmCIF format, chain FB [auth R] mmCIF format, chain VB [auth S]	FB [auth R], VB [auth S]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain FB [auth R] Focus chain VB [auth S] Interactions & Density Focus chain FB [auth R] Focus chain VB [auth S]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.53 Å
R-Value Free: 0.132 (Depositor), 0.130 (DCC)
R-Value Work: 0.082 (Depositor), 0.080 (DCC)
R-Value Observed: 0.085 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 161.789	α = 90
b = 171.331	β = 121.55
c = 122.484	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-3000	data reduction
SCALEPACK	data scaling
MOLREP	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2015-06-24

Deposition Author(s):

Wang, J.

Lomkalin, I.V.

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM022778

Revision History (Full details and data files)

Version 1.0: 2015-06-24
Type: Initial release
Version 1.1: 2018-02-14
Changes: Advisory, Author supporting evidence, Derived calculations, Source and taxonomy
Version 1.2: 2019-12-25
Changes: Author supporting evidence
Version 1.3: 2023-09-27
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.4: 2024-10-23
Changes: Structure summary