4DIO | pdb_00004dio

The crystal structure of transhydrogenase from Sinorhizobium meliloti

• PDB DOI: https://doi.org/10.2210/pdb4DIO/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Sinorhizobium meliloti SM11
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2012-01-31 Released: 2012-03-21 
• Deposition Author(s): Zhang, Z., Chamala, S., Evans, B., Foti, R., Gizzi, A., Hillerich, B., Kar, A., Lafleur, J., Seidel, R., Villigas, G., Zencheck, W., Almo, S.C., Swaminathan, S., New York Structural Genomics Research Consortium (NYSGRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 
  0.287 (Depositor), 0.280 (DCC) 
• R-Value Work: 
  0.232 (Depositor), 0.230 (DCC) 
• R-Value Observed: 
  0.235 (Depositor) 

Starting Model: experimental

Literature

The crystal structure of transhydrogenase from Sinorhizobium meliloti

Zhang, Z., Almo, S.C., Swaminathan, S.

To be published.

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 86.38 kDa 
• Atom Count: 4,994 
• Modeled Residue Count: 678 
• Deposited Residue Count: 810 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NAD(P) transhydrogenase subunit alpha part 1	A, B	405	Sinorhizobium meliloti SM11	Mutation(s): 0  Gene Names: pntAa, SM11_chr3030 EC: 1.6.1.2 (PDB Primary Data), 7.1.1.1 (UniProt)
UniProt
Find proteins for F7X914 (Sinorhizobium meliloti (strain SM11)) Explore F7X914  Go to UniProtKB:  F7X914

Small Molecules

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: 2.60 Å
• R-Value Free:  0.287 (Depositor), 0.280 (DCC) 
• R-Value Work:  0.232 (Depositor), 0.230 (DCC) 
• R-Value Observed: 0.235 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.777	α = 90
b = 69.67	β = 90
c = 138.387	γ = 90

Software Package:

Software Name	Purpose
CBASS	data collection
PHASER	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-03-21 
Deposition Author(s): Zhang, Z., Chamala, S., Evans, B., Foti, R., Gizzi, A., Hillerich, B., Kar, A., Lafleur, J., Seidel, R., Villigas, G., Zencheck, W., Almo, S.C., Swaminathan, S., New York Structural Genomics Research Consortium (NYSGRC)

Revision History  

• Version 1.0: 2012-03-21
  Type: Initial release
  
• Version 1.1: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.2: 2023-12-06
  Changes: Data collection
• Version 1.3: 2024-11-27
  Changes: Structure summary