3NX4 | pdb_00003nx4

Crystal structure of the yhdH oxidoreductase from Salmonella enterica in complex with NADP

• PDB DOI: https://doi.org/10.2210/pdb3NX4/pdb

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


• Deposited: 2010-07-12 Released: 2010-08-04 
• Deposition Author(s): Anderson, S.M., Wawrzak, Z., Peterson, S., Onopriyenko, O., Skarina, T., Anderson, W.F., Savchenko, A., Center for Structural Genomics of Infectious Diseases (CSGID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.191 (Depositor), 0.208 (DCC) 
• R-Value Work: 
  0.155 (Depositor), 0.185 (DCC) 
• R-Value Observed: 
  0.156 (Depositor) 

Literature

Crystal structure of the yhdH oxidoreductase from Salmonella enterica in complex with NADP

Anderson, S.M., Wawrzak, Z., Peterson, S., Onopriyenko, O., Skarina, T., Anderson, W.F., Savchenko, 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: 71.09 kDa 
• Atom Count: 5,355 
• Modeled Residue Count: 648 
• Deposited Residue Count: 648 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative oxidoreductase	A, B	324	Salmonella enterica subsp. enterica serovar Typhimurium str. LT2	Mutation(s): 0  Gene Names: yhdH, STM3376
UniProt
Find proteins for Q7CPM2 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)) Explore Q7CPM2  Go to UniProtKB:  Q7CPM2

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAP	C [auth A], D [auth B]	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C21 H28 N7 O17 P3 XJLXINKUBYWONI-NNYOXOHSSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.191 (Depositor), 0.208 (DCC) 
• R-Value Work:  0.155 (Depositor), 0.185 (DCC) 
• R-Value Observed: 0.156 (Depositor) 

Diffraction Data: https://doi.org/10.18430/m33nx4

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 103.218	α = 90
b = 122.364	β = 121.1
c = 64.912	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
BLU-MAX	data collection
HKL-2000	data reduction
HKL-2000	data scaling
SHELXS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-08-04 
Deposition Author(s): Anderson, S.M., Wawrzak, Z., Peterson, S., Onopriyenko, O., Skarina, T., Anderson, W.F., Savchenko, A., Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History  

• Version 1.0: 2010-08-04
  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: 2024-11-06
  Changes: Data collection, Database references, Derived calculations, Structure summary