6OMZ | pdb_00006omz

Crystal Structure of Dihydropteroate synthase from Mycobacterium smegmatis with bound 6-hydroxymethylpterin-monophosphate

PDB DOI: https://doi.org/10.2210/pdb6OMZ/pdb

Classification: LIGASE
Organism(s): Mycolicibacterium smegmatis MKD8
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2019-04-19 Released: 2019-05-08
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.85 Å
R-Value Free:
0.186 (Depositor), 0.190 (DCC)
R-Value Work:
0.151 (Depositor), 0.150 (DCC)
R-Value Observed:
0.154 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Crystal Structure of Dihydropteroate synthase from Mycobacterium smegmatis with bound 6-hydroxymethylpterin-monophosphate

Bolejack, M.J., Dranow, D.M., Lorimer, D.D., Horanyi, P.S., Edwards, T.E.

To be published.

Macromolecule Content

Total Structure Weight: 31.75 kDa
Atom Count: 2,436
Modeled Residue Count: 274
Deposited Residue Count: 293
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dihydropteroate synthase	A	293	Mycolicibacterium smegmatis MKD8	Mutation(s): 1 Gene Names: D806_059810 EC: 2.5.1.15
UniProt
Find proteins for A0A2U9PYL8 (Mycolicibacterium smegmatis (strain MKD8)) Explore A0A2U9PYL8 Go to UniProtKB: A0A2U9PYL8
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A2U9PYL8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PMM Query on PMM Download Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	PTERIN-6-YL-METHYL-MONOPHOSPHATE C₇ H₈ N₅ O₅ P AJXFJEHKGGCFNM-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
CIT Query on CIT Download Ideal Coordinates CCD File SDF format, chain B [auth A] SDF format, chain E [auth A] MOL2 format, chain B [auth A] MOL2 format, chain E [auth A] mmCIF format, chain B [auth A] mmCIF format, chain E [auth A]	B [auth A], E [auth A]	CITRIC ACID C₆ H₈ O₇ KRKNYBCHXYNGOX-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Focus chain E [auth A] Interactions & Density Focus chain B [auth A] Focus chain E [auth A]
DMS Query on DMS Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	DIMETHYL SULFOXIDE C₂ H₆ O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain M [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain M [auth A]	F [auth A] G [auth A] H [auth A] I [auth A] J [auth A] F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A]