3HJ9 | pdb_00003hj9

Crystal structure of a putative nitroreductase (reut_a1228) from ralstonia eutropha jmp134 at 2.00 A resolution

• PDB DOI: https://doi.org/10.2210/pdb3HJ9/pdb

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


• Deposited: 2009-05-21 Released: 2009-06-16 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.208 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.174 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.176 (Depositor) 

Literature

Crystal structure of oxidoreductase (YP_295443.1) from RALSTONIA EUTROPHA JMP134 at 2.00 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)

Macromolecule Content 

• Total Structure Weight: 50.82 kDa 
• Atom Count: 3,657 
• Modeled Residue Count: 425 
• Deposited Residue Count: 446 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Oxidoreductase	A, B	223	Cupriavidus pinatubonensis JMP134	Mutation(s): 0  Gene Names: Reut_A1228, YP_295443.1
UniProt
Find proteins for Q472T4 (Cupriavidus pinatubonensis (strain JMP 134 / LMG 1197)) Explore Q472T4  Go to UniProtKB:  Q472T4

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FMN	C [auth A], F [auth B]	FLAVIN MONONUCLEOTIDE C17 H21 N4 O9 P FVTCRASFADXXNN-SCRDCRAPSA-N
MPD	E [auth A]	(4S)-2-METHYL-2,4-PENTANEDIOL C6 H14 O2 SVTBMSDMJJWYQN-YFKPBYRVSA-N
ACT	D [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
MG	G [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

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: 2.00 Å
• R-Value Free:  0.208 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.174 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.176 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M33HJ9

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.865	α = 90
b = 78.865	β = 90
c = 136.555	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SOLVE	phasing
MolProbity	model building
SCALA	data scaling
PDB_EXTRACT	data extraction
MOSFLM	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-06-16 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2009-06-16
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Source and taxonomy, Version format compliance
• Version 1.2: 2017-11-01
  Changes: 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: 2024-11-06
  Changes: Data collection, Structure summary