3PP8 | pdb_00003pp8

2.1 Angstrom Crystal Structure of Putative Oxidoreductase (ycdW) from Salmonella typhimurium

• PDB DOI: https://doi.org/10.2210/pdb3PP8/pdb

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


• Deposited: 2010-11-24 Released: 2010-12-08 
• Deposition Author(s): Minasov, G., Wawrzak, Z., Skarina, T., Wang, Y., Papazisi, L., Savchenko, A., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.235 (Depositor), 0.236 (DCC) 
• R-Value Work: 
  0.197 (Depositor), 0.204 (DCC) 
• R-Value Observed: 
  0.199 (Depositor) 

Starting Model: experimental

Literature

2.1 Angstrom Crystal Structure of Putative Oxidoreductase (ycdW) from Salmonella typhimurium.

Minasov, G., Wawrzak, Z., Skarina, T., Wang, Y., Papazisi, L., Savchenko, A., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

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: 35.72 kDa 
• Atom Count: 2,549 
• Modeled Residue Count: 310 
• Deposited Residue Count: 315 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glyoxylate/hydroxypyruvate reductase A	A	315	Salmonella enterica subsp. enterica serovar Typhimurium str. LT2	Mutation(s): 0  Gene Names: ghrA, STM1135, ycdW EC: 1.1.1.79 (PDB Primary Data), 1.1.1.81 (PDB Primary Data)
UniProt
Find proteins for Q8ZQ30 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)) Explore Q8ZQ30  Go to UniProtKB:  Q8ZQ30

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.235 (Depositor), 0.236 (DCC) 
• R-Value Work:  0.197 (Depositor), 0.204 (DCC) 
• R-Value Observed: 0.199 (Depositor) 

Diffraction Data: https://doi.org/10.18430/m33pp8

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 40.495	α = 90
b = 139.371	β = 90
c = 111.043	γ = 90

Software Package:

Software Name	Purpose
Blu-Ice	data collection
PHENIX	model building
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-12-08 
Deposition Author(s): Minasov, G., Wawrzak, Z., Skarina, T., Wang, Y., Papazisi, L., Savchenko, A., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History  

• Version 1.0: 2010-12-08
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-11-08
  Changes: Refinement description
• Version 1.3: 2023-09-06
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.4: 2023-12-06
  Changes: Data collection
• Version 1.5: 2024-11-06
  Changes: Structure summary