3IUP | pdb_00003iup

Crystal structure of Putative NADPH:quinone oxidoreductase (YP_296108.1) from RALSTONIA EUTROPHA JMP134 at 1.70 A resolution

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 
    0.208 (Depositor), 0.213 (DCC) 
  • R-Value Work: 
    0.175 (Depositor), 0.179 (DCC) 
  • R-Value Observed: 
    0.176 (Depositor) 

wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


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

Literature

Crystal structure of Putative NADPH:quinone oxidoreductase (YP_296108.1) from RALSTONIA EUTROPHA JMP134 at 1.70 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Macromolecule Content 

  • Total Structure Weight: 83.6 kDa 
  • Atom Count: 6,446 
  • Modeled Residue Count: 751 
  • Deposited Residue Count: 758 
  • Unique protein chains: 1

Macromolecules

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|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Putative NADPH:quinone oxidoreductase
A, B
379Cupriavidus pinatubonensis JMP134Mutation(s): 0 
Gene Names: Reut_A1899, YP_296108.1
UniProt
Find proteins for Q470B9 (Cupriavidus pinatubonensis (strain JMP 134 / LMG 1197))
Explore Q470B9 
Go to UniProtKB:  Q470B9
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ470B9
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NDP

Query on NDP


Download:Ideal Coordinates CCD File
C [auth A],
J [auth B]		NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H30 N7 O17 P3
ACFIXJIJDZMPPO-NNYOXOHSSA-N
EDO

Query on EDO


Download:Ideal Coordinates CCD File
D [auth A]
E [auth A]
F [auth A]
K [auth B]
L [auth B]
D [auth A],
E [auth A],
F [auth A],
K [auth B],
L [auth B],
M [auth B],
N [auth B],
O [auth B],
P [auth B]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
ACT

Query on ACT


Download:Ideal Coordinates CCD File
G [auth A],
H [auth A],
I [auth A]		ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A, B
L-PEPTIDE LINKINGC5 H11 N O2 SeMET

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free:  0.208 (Depositor), 0.213 (DCC) 
  • R-Value Work:  0.175 (Depositor), 0.179 (DCC) 
  • R-Value Observed: 0.176 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 60.484α = 90
b = 77.927β = 109.21
c = 85.447γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PHENIXrefinement
SHELXphasing
MolProbitymodel building
XSCALEdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
SHELXDphasing
autoSHARPphasing

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-09-15
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Source and taxonomy, Version format compliance
  • Version 1.2: 2017-10-25
    Changes: Author supporting evidence, Refinement description
  • Version 1.3: 2019-07-24
    Changes: Data collection, Derived calculations, Refinement description
  • Version 1.4: 2023-02-01
    Changes: Database references, Derived calculations
  • Version 1.5: 2024-11-20
    Changes: Data collection, Refinement description, Structure summary