3IUP

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

• PDB DOI: https://doi.org/10.2210/pdb3IUP/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Cupriavidus pinatubonensis JMP134
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-08-31 Released: 2009-09-15 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.208 
• R-Value Work: 0.175 
• R-Value Observed: 0.176 

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.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative NADPH:quinone oxidoreductase	A, B	379	Cupriavidus pinatubonensis JMP134	Mutation(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

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NDP	C [auth A], J [auth B]	NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C21 H30 N7 O17 P3 ACFIXJIJDZMPPO-NNYOXOHSSA-N
EDO	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	G [auth A], H [auth A], I [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

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: 1.70 Å
• R-Value Free: 0.208 
• R-Value Work: 0.175 
• R-Value Observed: 0.176 
• Space Group: P 1 2₁ 1
• Diffraction Data: https://doi.org/10.18430/M33IUP

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.484	α = 90
b = 77.927	β = 109.21
c = 85.447	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SHELX	phasing
MolProbity	model building
XSCALE	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
SHELXD	phasing
autoSHARP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-09-15 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• 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