3HWR | pdb_00003hwr

Crystal structure of PanE/ApbA family ketopantoate reductase (YP_299159.1) from Ralstonia eutropha JMP134 at 2.15 A resolution

• PDB DOI: https://doi.org/10.2210/pdb3HWR/pdb

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


• Deposited: 2009-06-18 Released: 2009-06-30 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free: 
  0.226 (Depositor), 0.227 (DCC) 
• R-Value Work: 
  0.183 (Depositor), 0.184 (DCC) 
• R-Value Observed: 
  0.186 (Depositor) 

Literature

Crystal structure of PanE/ApbA family ketopantoate reductase (YP_299159.1) from Ralstonia eutropha JMP134 at 2.15 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: 70.87 kDa 
• Atom Count: 4,838 
• Modeled Residue Count: 597 
• Deposited Residue Count: 636 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
2-dehydropantoate 2-reductase	A, B	318	Cupriavidus pinatubonensis JMP134	Mutation(s): 0  Gene Names: Reut_B4967, YP_299159.1 EC: 1.1.1.169
UniProt
Find proteins for Q46RB9 (Cupriavidus pinatubonensis (strain JMP 134 / LMG 1197)) Explore Q46RB9  Go to UniProtKB:  Q46RB9

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NDP	C [auth A], F [auth B]	NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C21 H30 N7 O17 P3 ACFIXJIJDZMPPO-NNYOXOHSSA-N
BCN	D [auth A], G [auth B]	BICINE C6 H13 N O4 FSVCELGFZIQNCK-UHFFFAOYSA-N
MRD	E [auth A], H [auth B]	(4R)-2-METHYLPENTANE-2,4-DIOL C6 H14 O2 SVTBMSDMJJWYQN-RXMQYKEDSA-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: 2.15 Å
• R-Value Free:  0.226 (Depositor), 0.227 (DCC) 
• R-Value Work:  0.183 (Depositor), 0.184 (DCC) 
• R-Value Observed: 0.186 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M33HWR

Space Group: P 6₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 116.21	α = 90
b = 116.21	β = 90
c = 95.604	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-06-30 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2009-06-30
  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: 2024-11-20
  Changes: Data collection, Refinement description, Structure summary