4PMJ | pdb_00004pmj

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

• PDB DOI: https://doi.org/10.2210/pdb4PMJ/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Sinorhizobium meliloti 1021
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2014-05-21 Released: 2014-06-11 
• Deposition Author(s): Gasiorowska, O.A., Shabalin, I.G., Handing, K.B., Szlachta, K., Zimmerman, M.D., Hillerich, B.S., Gizzi, A., Toro, R., Bonanno, J., Seidel, R., Almo, S.C., Minor, W., New York Structural Genomics Research Consortium (NYSGRC)
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.217 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.167 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.170 (Depositor) 

Literature

Crystal structure of a putative oxidoreductase from Sinorhizobiummeliloti 1021 in complex with NADP

Gasiorowska, O.A., Shabalin, I.G., Handing, K.B., Szlachta, K., Zimmerman, M.D., Hillerich, B.S., Gizzi, A., Toro, R., Bonanno, J., Seidel, R., Almo, S.C., Minor, W.

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: 31.92 kDa 
• Atom Count: 2,305 
• Modeled Residue Count: 281 
• Deposited Residue Count: 281 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative oxidoreductase	A	281	Sinorhizobium meliloti 1021	Mutation(s): 0  Gene Names: R02112, SMc01429 EC: 1.1.1
UniProt
Find proteins for Q92NR7 (Rhizobium meliloti (strain 1021)) Explore Q92NR7  Go to UniProtKB:  Q92NR7

Small Molecules

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

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: 2.20 Å
• R-Value Free:  0.217 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.167 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.170 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M3MW27

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.324	α = 90
b = 78.897	β = 90
c = 79.563	γ = 90

Software Package:

Software Name	Purpose
HKL-3000	data collection
HKL-3000	phasing
HKL-3000	data scaling
SHELXDE	phasing
MLPHARE	phasing
DM	phasing
Coot	model building
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2014-06-11 
Deposition Author(s): Gasiorowska, O.A., Shabalin, I.G., Handing, K.B., Szlachta, K., Zimmerman, M.D., Hillerich, B.S., Gizzi, A., Toro, R., Bonanno, J., Seidel, R., Almo, S.C., Minor, W., New York Structural Genomics Research Consortium (NYSGRC)

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	NIH-5U54GM094662-04

Revision History  

• Version 1.0: 2014-06-11
  Type: Initial release
  
• Version 1.1: 2015-08-26
  Changes: Data collection
• Version 1.2: 2017-09-20
  Changes: Author supporting evidence, Derived calculations, Refinement description
• Version 1.3: 2019-12-25
  Changes: Author supporting evidence
• Version 1.4: 2022-04-13
  Changes: Data collection, Database references, Structure summary
• Version 1.5: 2023-12-27
  Changes: Data collection
• Version 1.6: 2024-11-06
  Changes: Structure summary