5EVC | pdb_00005evc

Crystal structure of putative aspartate racemase from Salmonella Typhimurium complexed with sulfate and potassium

• PDB DOI: https://doi.org/10.2210/pdb5EVC/pdb

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


• Deposited: 2015-11-19 Released: 2015-12-02 
• Deposition Author(s): Maltseva, N., Kim, Y., Stam, J., Anderson, W.F., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.157 (Depositor), 0.145 (DCC) 
• R-Value Work: 
  0.135 (Depositor), 0.135 (DCC) 
• R-Value Observed: 
  0.137 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of putative aspartate racemase from Salmonella Typhimurium complexed with sulfate and potassium

Maltseva, N., Kim, Y., Stam, J., Anderson, W.F., Joachimiak, A.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 58.88 kDa 
• Atom Count: 4,024 
• Modeled Residue Count: 475 
• Deposited Residue Count: 536 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative aspartate racemase	A, B	268	Salmonella enterica subsp. enterica serovar Typhimurium str. LT2	Mutation(s): 0  Gene Names: STM4510
UniProt
Find proteins for Q8ZJZ9 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)) Explore Q8ZJZ9  Go to UniProtKB:  Q8ZJZ9

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	D [auth A], J [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	F [auth A], L [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
FMT	G [auth A]	FORMIC ACID C H2 O2 BDAGIHXWWSANSR-UHFFFAOYSA-N
K	C [auth A], E [auth A], I [auth B], M [auth B]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N
CL	H [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
F	K [auth B]	FLUORIDE ION F KRHYYFGTRYWZRS-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.157 (Depositor), 0.145 (DCC) 
• R-Value Work:  0.135 (Depositor), 0.135 (DCC) 
• R-Value Observed: 0.137 (Depositor) 

Diffraction Data: https://doi.org/10.18430/m35evc

Space Group: P 6₅

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 85.328	α = 90
b = 85.328	β = 90
c = 113.997	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2015-12-02 
Deposition Author(s): Maltseva, N., Kim, Y., Stam, J., Anderson, W.F., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

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

Revision History  

• Version 1.0: 2015-12-02
  Type: Initial release
  
• Version 1.1: 2019-11-27
  Changes: Author supporting evidence, Derived calculations, Structure summary
• Version 1.2: 2023-09-27
  Changes: Data collection, Database references, Derived calculations, Refinement description