4NH4 | pdb_00004nh4

Structure of the binary complex of a zingiber officinale double bond reductase in complex with NADP

• PDB DOI: https://doi.org/10.2210/pdb4NH4/pdb

• Classification: PLANT PROTEIN
• Organism(s): Zingiber officinale
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2013-11-04 Released: 2014-11-05 
• Deposition Author(s): 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: 2.10 Å
• R-Value Free: 
  0.260 (Depositor), 0.263 (DCC) 
• R-Value Work: 
  0.193 (Depositor), 0.201 (DCC) 
• R-Value Observed: 
  0.196 (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)

Macromolecule Content 

• Total Structure Weight: 81.46 kDa 
• Atom Count: 5,835 
• Modeled Residue Count: 703 
• Deposited Residue Count: 716 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Zingiber officinale double bond reductase	A, B	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	C [auth A], D [auth B]	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C21 H28 N7 O17 P3 XJLXINKUBYWONI-NNYOXOHSSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.260 (Depositor), 0.263 (DCC) 
• R-Value Work:  0.193 (Depositor), 0.201 (DCC) 
• R-Value Observed: 0.196 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.66	α = 90
b = 78.406	β = 90
c = 155.706	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
DNA	data collection
XDS	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-11-05 
Deposition Author(s): 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: 2014-11-05
  Type: Initial release
  
• Version 1.1: 2023-11-08
  Changes: Data collection, Database references, Derived calculations, Refinement description