4WE3 | pdb_00004we3

STRUCTURE OF THE BINARY COMPLEX OF A ZINGIBER OFFICINALE DOUBLE BOND REDUCTASE IN COMPLEX WITH NADP MONOCLINIC CRYSTAL FORM

• PDB DOI: https://doi.org/10.2210/pdb4WE3/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Zingiber officinale
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2014-09-09 Released: 2015-09-30 
• Deposition Author(s): Collery, J., Langlois d'Estaintot, B., Buratto, J., Granier, T., Gallois, B., Willis, M.A., Sang, Y., Flores-Sanchez, I.J., Gang, D.R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 
  0.265 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.222 (Depositor), 0.220 (DCC) 
• R-Value Observed: 
  0.225 (Depositor) 

Starting Model: experimental

Literature

STRUCTURE OF ZINGIBER OFFICINALE DOUBLE BOND REDUCTASE

Buratto, J., Langlois d'Estaintot, B., Granier, T., Gallois, B., Willis, M.A., Sang, Y., Flores-Sanchez, I.J., Gang, D.R.

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 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 162.93 kDa 
• Atom Count: 10,479 
• Modeled Residue Count: 1,367 
• Deposited Residue Count: 1,432 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Double Bond Reductase	A, B, C, D	358	Zingiber officinale	Mutation(s): 0
UniProt
Find proteins for A0A096LNF0 (Zingiber officinale) Explore A0A096LNF0  Go to UniProtKB:  A0A096LNF0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAP	E [auth A], F [auth B], G [auth C], H [auth D]	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C21 H28 N7 O17 P3 XJLXINKUBYWONI-NNYOXOHSSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free:  0.265 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.222 (Depositor), 0.220 (DCC) 
• R-Value Observed: 0.225 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 131.704	α = 90
b = 133.447	β = 101.39
c = 90.942	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
REFMAC	refinement
PDB_EXTRACT	data extraction
XSCALE	data scaling
PHASER	phasing
XSCALE	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-09-30 
Deposition Author(s): Collery, J., Langlois d'Estaintot, B., Buratto, J., Granier, T., Gallois, B., Willis, M.A., Sang, Y., Flores-Sanchez, I.J., Gang, D.R.

Revision History  

• Version 1.0: 2015-09-30
  Type: Initial release
  
• Version 1.1: 2019-06-12
  Changes: Data collection, Database references, Structure summary
• Version 1.2: 2024-01-10
  Changes: Data collection, Database references, Refinement description