4PMJ

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

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.167 
  • R-Value Observed: 0.170 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.5 of the entry. See complete history. 


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.

Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Putative oxidoreductase281Sinorhizobium meliloti 1021Mutation(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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ92NR7
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAP
Query on NAP
Download Ideal Coordinates CCD File 
B [auth A]NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H28 N7 O17 P3
XJLXINKUBYWONI-NNYOXOHSSA-N
GOL
Query on GOL
Download Ideal Coordinates CCD File 
C [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 44.324α = 90
b = 78.897β = 90
c = 79.563γ = 90
Software Package:
Software NamePurpose
HKL-3000data collection
HKL-3000phasing
HKL-3000data scaling
SHELXDEphasing
MLPHAREphasing
DMphasing
Cootmodel building
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesNIH-5U54GM094662-04

Revision History  (Full details and data files)

  • 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