4ESO | pdb_00004eso

Crystal structure of a putative oxidoreductase protein from Sinorhizobium meliloti 1021 in complex with NADP

• PDB DOI: https://doi.org/10.2210/pdb4ESO/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Sinorhizobium meliloti 1021
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2012-04-23 Released: 2012-05-16 
• Deposition Author(s): Ghosh, A., Bhoshle, R., Toro, R., Gizzi, A., Hillerich, B., Seidel, R., Almo, S.C., New York Structural Genomics Research Consortium (NYSGRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.91 Å
• R-Value Free: 
  0.234 (Depositor), 0.229 (DCC) 
• R-Value Work: 
  0.193 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.195 (Depositor) 

Literature

Crystal structure of a putative oxidoreductase protein from Sinorhizobium meliloti 1021 in complex with NADP

Ghosh, A., Bhoshle, R., Toro, R., Gizzi, A., Hillerich, B., Seidel, R., Almo, S.C.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 110.62 kDa 
• Atom Count: 7,996 
• Modeled Residue Count: 990 
• Deposited Residue Count: 1,020 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative oxidoreductase	A, B, C, D	255	Sinorhizobium meliloti 1021	Mutation(s): 0  Gene Names: R02322, SMc01571 EC: 1
UniProt
Find proteins for Q92N93 (Rhizobium meliloti (strain 1021)) Explore Q92N93  Go to UniProtKB:  Q92N93

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAP	E [auth A], F [auth B], H [auth C], J [auth D]	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C21 H28 N7 O17 P3 XJLXINKUBYWONI-NNYOXOHSSA-N
GOL	G [auth B], I [auth C]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.91 Å
• R-Value Free:  0.234 (Depositor), 0.229 (DCC) 
• R-Value Work:  0.193 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.195 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.96	α = 66.5
b = 66.74	β = 78.3
c = 70.54	γ = 62.96

Software Package:

Software Name	Purpose
CBASS	data collection
SOLVE	phasing
PHENIX	refinement
HKL-3000	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-05-16 
Deposition Author(s): Ghosh, A., Bhoshle, R., Toro, R., Gizzi, A., Hillerich, B., Seidel, R., Almo, S.C., New York Structural Genomics Research Consortium (NYSGRC)

Revision History  

• Version 1.0: 2012-05-16
  Type: Initial release
  
• Version 1.1: 2024-11-27
  Changes: Data collection, Database references, Derived calculations, Structure summary