6WON | pdb_00006won

Crystal structure of acetoin dehydrogenase YohF from Salmonella typhimurium

PDB DOI: https://doi.org/10.2210/pdb6WON/pdb

Classification: OXIDOREDUCTASE
Organism(s): Salmonella enterica subsp. enterica serovar Typhimurium str. LT2
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2020-04-25 Released: 2020-05-13
Deposition Author(s): Stogios, P.J., Skarina, T., Mesa, N., Endres, M., Savchenko, A., Joachimiak, A., Satchell, K.J.F., Center for Structural Genomics of Infectious Diseases (CSGID)
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.13 Å
R-Value Free:
0.207 (Depositor), 0.202 (DCC)
R-Value Work:
0.160 (Depositor), 0.159 (DCC)
R-Value Observed:
0.161 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of acetoin dehydrogenase YohF from Salmonella typhimurium

Stogios, P.J.

To be published.

Macromolecule Content

Total Structure Weight: 216.57 kDa
Atom Count: 15,700
Modeled Residue Count: 1,946
Deposited Residue Count: 2,040
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
YohF	A, B, C, D, E A, B, C, D, E, F, G, H	255	Salmonella enterica subsp. enterica serovar Typhimurium str. LT2	Mutation(s): 0 Gene Names: yohF, STM2171 EC: 1
UniProt
Find proteins for Q8ZNM5 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)) Explore Q8ZNM5 Go to UniProtKB: Q8ZNM5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8ZNM5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain J [auth F] SDF format, chain I [auth A] MOL2 format, chain J [auth F] MOL2 format, chain I [auth A] mmCIF format, chain J [auth F] mmCIF format, chain I [auth A]	I [auth A], J [auth F]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain I [auth A] Focus chain J [auth F] Interactions & Density Focus chain I [auth A] Focus chain J [auth F]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain K [auth G] MOL2 format, chain K [auth G] mmCIF format, chain K [auth G]	K [auth G]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain K [auth G] Interactions & Density Focus chain K [auth G]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.13 Å
R-Value Free: 0.207 (Depositor), 0.202 (DCC)
R-Value Work: 0.160 (Depositor), 0.159 (DCC)
R-Value Observed: 0.161 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 72.549	α = 90
b = 114.171	β = 90
c = 219.342	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHASER	phasing
Coot	model building

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2020-05-13

Deposition Author(s):

Satchell, K.J.F.

Center for Structural Genomics of Infectious Diseases (CSGID)

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	HHSN272201700060C

Revision History (Full details and data files)

Version 1.0: 2020-05-13
Type: Initial release
Version 1.1: 2023-10-18
Changes: Data collection, Database references, Refinement description

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.