4MKR | pdb_00004mkr

Structure of the apo form of a Zingiber officinale double bond reductase

• PDB DOI: https://doi.org/10.2210/pdb4MKR/pdb

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


• Deposited: 2013-09-05 Released: 2014-09-10 
• Deposition Author(s): Buratto, J., Langlois d'Estaintot, B., 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: 2.58 Å
• R-Value Free: 
  0.282 (Depositor), 0.280 (DCC) 
• R-Value Work: 
  0.228 (Depositor), 0.230 (DCC) 
• R-Value Observed: 
  0.231 (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: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 Pseudo Symmetry: Cyclic - C2  (Explore in 3D)
Pseudo 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: 159.96 kDa 
• Atom Count: 9,244 
• Modeled Residue Count: 1,213 
• Deposited Residue Count: 1,432 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Zingiber officinale 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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.58 Å
• R-Value Free:  0.282 (Depositor), 0.280 (DCC) 
• R-Value Work:  0.228 (Depositor), 0.230 (DCC) 
• R-Value Observed: 0.231 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.93	α = 80.15
b = 76.34	β = 89.97
c = 93.45	γ = 85.66

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-09-10 
Deposition Author(s): Buratto, J., Langlois d'Estaintot, B., Granier, T., Gallois, B., Willis, M.A., Sang, Y., Flores-Sanchez, I.J., Gang, D.R.

Revision History  

• Version 1.0: 2014-09-10
  Type: Initial release
  
• Version 1.1: 2023-09-20
  Changes: Data collection, Database references, Refinement description