4IYH | pdb_00004iyh

The crystal structure of a secreted protein EsxB (SeMet-labeled, C-term. His-Tagged) from Bacillus anthracis str. Sterne

PDB DOI: https://doi.org/10.2210/pdb4IYH/pdb

Classification: UNKNOWN FUNCTION
Organism(s): Bacillus anthracis str. Sterne
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2013-01-28 Released: 2013-02-20
Deposition Author(s): Fan, Y., Tan, K., Chhor, G., Jedrzejczak, R., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.88 Å
R-Value Free:
0.162 (Depositor), 0.146 (DCC)
R-Value Work:
0.141 (Depositor), 0.133 (DCC)
R-Value Observed:
0.145 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

The crystal structure of a secreted protein EsxB (SeMet-labeled, C-term. His-Tagged) from Bacillus anthracis str. Sterne

Fan, Y., Tan, K., Chhor, G., Jedrzejczak, R., Joachimiak, A.

To be published.

Macromolecule Content

Total Structure Weight: 45.66 kDa
Atom Count: 2,757
Modeled Residue Count: 322
Deposited Residue Count: 392
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Secreted protein EsxB	A, B, C, D	98	Bacillus anthracis str. Sterne	Mutation(s): 0 Gene Names: Bacillus anthracis
UniProt
Find proteins for A0A6L7HJC4 (Bacillus anthracis) Explore A0A6L7HJC4 Go to UniProtKB: A0A6L7HJC4
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A6L7HJC4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain R [auth D] SDF format, chain Q [auth D] SDF format, chain O [auth C] SDF format, chain K [auth B] SDF format, chain J [auth B] SDF format, chain I [auth A] SDF format, chain H [auth A] MOL2 format, chain R [auth D] MOL2 format, chain Q [auth D] MOL2 format, chain O [auth C] MOL2 format, chain K [auth B] MOL2 format, chain J [auth B] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] mmCIF format, chain R [auth D] mmCIF format, chain Q [auth D] mmCIF format, chain O [auth C] mmCIF format, chain K [auth B] mmCIF format, chain J [auth B] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A]	H [auth A] I [auth A] J [auth B] K [auth B] O [auth C] H [auth A], I [auth A], J [auth B], K [auth B], O [auth C], Q [auth D], R [auth D]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain O [auth C] Focus chain Q [auth D] Focus chain R [auth D] Interactions & Density Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain O [auth C] Focus chain Q [auth D] Focus chain R [auth D]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain L [auth C] SDF format, chain E [auth A] MOL2 format, chain L [auth C] MOL2 format, chain E [auth A] mmCIF format, chain L [auth C] mmCIF format, chain E [auth A]	E [auth A], L [auth C]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain L [auth C] Interactions & Density Focus chain E [auth A] Focus chain L [auth C]
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain N [auth C] SDF format, chain G [auth A] MOL2 format, chain N [auth C] MOL2 format, chain G [auth A] mmCIF format, chain N [auth C] mmCIF format, chain G [auth A]	G [auth A], N [auth C]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain G [auth A] Focus chain N [auth C] Interactions & Density Focus chain G [auth A] Focus chain N [auth C]
FMT Query on FMT Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain M [auth C] SDF format, chain P [auth D] MOL2 format, chain F [auth A] MOL2 format, chain M [auth C] MOL2 format, chain P [auth D] mmCIF format, chain F [auth A] mmCIF format, chain M [auth C] mmCIF format, chain P [auth D]	F [auth A], M [auth C], P [auth D]	FORMIC ACID C H₂ O₂ BDAGIHXWWSANSR-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain M [auth C] Focus chain P [auth D] Interactions & Density Focus chain F [auth A] Focus chain M [auth C] Focus chain P [auth D]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B, C, D	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.88 Å
R-Value Free: 0.162 (Depositor), 0.146 (DCC)
R-Value Work: 0.141 (Depositor), 0.133 (DCC)
R-Value Observed: 0.145 (Depositor)

Space Group: P 3₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.337	α = 90
b = 77.337	β = 90
c = 71.226	γ = 120

Software Package:

Software Name	Purpose
SBC-Collect	data collection
SHELXD	phasing
MLPHARE	phasing
DM	model building
ARP	model building
WARP	model building
HKL-3000	phasing
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
DM	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2013-02-20

Deposition Author(s):

Midwest Center for Structural Genomics (MCSG)

Revision History (Full details and data files)

Version 1.0: 2013-02-20
Type: Initial release
Version 1.1: 2024-11-27
Changes: Data collection, Database references, Derived calculations, Structure summary