2CSG | pdb_00002csg

Crystal Structure of the Putative Oxidoreductase from Salmonella typhimurium LT2

• PDB DOI: https://doi.org/10.2210/pdb2CSG/pdb

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


• Deposited: 2005-05-21 Released: 2005-07-05 
• Deposition Author(s): Kim, Y., Li, H., Collart, F., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 
  0.237 (Depositor), 0.239 (DCC) 
• R-Value Work: 
  0.188 (Depositor), 0.189 (DCC) 
• R-Value Observed: 
  0.193 (Depositor) 

Literature

Crystal Structure of the Putative Oxidoreductase from Salmonella typhimurium LT2

Kim, Y., Li, H., Collart, F., Joachimiak, A.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 48.12 kDa 
• Atom Count: 3,552 
• Modeled Residue Count: 417 
• Deposited Residue Count: 424 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
putative cytoplasmic protein	A	424	Salmonella enterica subsp. enterica serovar Typhimurium str. LT2	Mutation(s): 0  Gene Names: ybiU
UniProt
Find proteins for Q8ZQM7 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)) Explore Q8ZQM7  Go to UniProtKB:  Q8ZQM7

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CIT	E [auth A]	CITRIC ACID C6 H8 O7 KRKNYBCHXYNGOX-UHFFFAOYSA-N
ICT	C [auth A]	ISOCITRIC ACID C6 H8 O7 ODBLHEXUDAPZAU-ZAFYKAAXSA-N
SIN	D [auth A]	SUCCINIC ACID C4 H6 O4 KDYFGRWQOYBRFD-UHFFFAOYSA-N
FE	B [auth A]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free:  0.237 (Depositor), 0.239 (DCC) 
• R-Value Work:  0.188 (Depositor), 0.189 (DCC) 
• R-Value Observed: 0.193 (Depositor) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 110.801	α = 90
b = 110.801	β = 90
c = 105.64	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
SBC-Collect	data collection
HKL-2000	data reduction
HKL-2000	data scaling
HKL-3000	phasing
SHELXD	phasing
SHELXE	model building
MLPHARE	phasing
SOLVE	phasing
RESOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-07-05 
Deposition Author(s): Kim, Y., Li, H., Collart, F., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2005-07-05
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Source and taxonomy, Version format compliance
• Version 1.3: 2024-02-14
  Changes: Data collection, Database references, Derived calculations