3R3S

Structure of the YghA Oxidoreductase from Salmonella enterica

PDB DOI: https://doi.org/10.2210/pdb3R3S/pdb

Classification: OXIDOREDUCTASE
Organism(s): Salmonella enterica subsp. enterica serovar Typhimurium
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2011-03-16 Released: 2011-03-30
Deposition Author(s): Anderson, S.M., Wawrzak, Z., Onopriyenko, O., Peterson, S.N., Anderson, W.F., Savchenko, A., Center for Structural Genomics of Infectious Diseases (CSGID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.25 Å
R-Value Free: 0.153
R-Value Work: 0.129
R-Value Observed: 0.130

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Structure of the YghA Oxidoreductase from Salmonella enterica

Anderson, S.M., Wawrzak, Z., Onopriyenko, O., Peterson, S.N., Anderson, W.F., Savchenko, A., Center for Structural Genomics of Infectious Diseases (CSGID)

To be published.

Macromolecule Content

Total Structure Weight: 128.91 kDa
Atom Count: 11,189
Modelled Residue Count: 1,168
Deposited Residue Count: 1,176
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
oxidoreductase	A, B, C, D	294	Salmonella enterica subsp. enterica serovar Typhimurium	Mutation(s): 0 Gene Names: yghA, STM3157
UniProt
Find proteins for Q8ZM09 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)) Explore Q8ZM09 Go to UniProtKB: Q8ZM09
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q8ZM09
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAD Query on NAD Download Ideal Coordinates CCD File SDF format, chain H [auth B] SDF format, chain O [auth D] SDF format, chain E [auth A] SDF format, chain L [auth C] MOL2 format, chain H [auth B] MOL2 format, chain O [auth D] MOL2 format, chain E [auth A] MOL2 format, chain L [auth C]	E [auth A], H [auth B], L [auth C], O [auth D]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C₂₁ H₂₇ N₇ O₁₄ P₂ BAWFJGJZGIEFAR-NNYOXOHSSA-N		Interactions Focus chain E [auth A] Focus chain H [auth B] Focus chain L [auth C] Focus chain O [auth D] Interactions & Density Focus chain E [auth A] Focus chain H [auth B] Focus chain L [auth C] Focus chain O [auth D]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain K [auth B] MOL2 format, chain K [auth B]	K [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain K [auth B] Interactions & Density Focus chain K [auth B]
FMT Query on FMT Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain I [auth B] SDF format, chain M [auth C] SDF format, chain P [auth D] MOL2 format, chain F [auth A] MOL2 format, chain I [auth B] MOL2 format, chain M [auth C] MOL2 format, chain P [auth D]	F [auth A], I [auth B], M [auth C], P [auth D]	FORMIC ACID C H₂ O₂ BDAGIHXWWSANSR-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain I [auth B] Focus chain M [auth C] Focus chain P [auth D] Interactions & Density Focus chain F [auth A] Focus chain I [auth B] Focus chain M [auth C] Focus chain P [auth D]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain J [auth B] SDF format, chain N [auth C] SDF format, chain Q [auth D] MOL2 format, chain G [auth A] MOL2 format, chain J [auth B] MOL2 format, chain N [auth C] MOL2 format, chain Q [auth D]	G [auth A], J [auth B], N [auth C], Q [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain J [auth B] Focus chain N [auth C] Focus chain Q [auth D] Interactions & Density Focus chain G [auth A] Focus chain J [auth B] Focus chain N [auth C] Focus chain Q [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.25 Å
R-Value Free: 0.153
R-Value Work: 0.129
R-Value Observed: 0.130
Space Group: P 1 2₁ 1
Diffraction Data: https://doi.org/10.18430/m33r3s

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 75.728	α = 90
b = 80.673	β = 100.96
c = 96.168	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
BLU-MAX	data collection
HKL-2000	data reduction
HKL-2000	data scaling
MrBUMP/MolRep	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2011-03-30

Deposition Author(s):

Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History (Full details and data files)

Version 1.0: 2011-03-30
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2023-09-13
Changes: Data collection, Database references, Derived calculations, Refinement description