5XSF | pdb_00005xsf

Crystal structure of the 2-keto-3-deoxy-6-phosphogluconate aldolase of Zymomonas mobilis ZM4 with 3-phosphoglycerate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.96 Å
  • R-Value Free: 
    0.212 (Depositor), 0.210 (DCC) 
  • R-Value Work: 
    0.191 (Depositor), 0.190 (DCC) 
  • R-Value Observed: 
    0.192 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted 3PGClick on this verticalbar to view detailsBest fitted 3PYClick on this verticalbar to view detailsBest fitted PO4Click on this verticalbar to view details

This is version 1.1 of the entry. See complete history


Literature

Crystal structure of the 2-keto-3-deoxy-6-phosphogluconate aldolase of Zymomonas mobilis ZM4

Seo, P.W.Kim, J.S.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
KHG/KDPG aldolase209Zymomonas mobilis subsp. mobilis ZM4 = ATCC 31821Mutation(s): 0 
Gene Names: edakdgAZMO0997
EC: 4.1.2.14
UniProt
Find proteins for Q00384 (Zymomonas mobilis subsp. mobilis (strain ATCC 31821 / ZM4 / CP4))
Explore Q00384 
Go to UniProtKB:  Q00384
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ00384
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.96 Å
  • R-Value Free:  0.212 (Depositor), 0.210 (DCC) 
  • R-Value Work:  0.191 (Depositor), 0.190 (DCC) 
  • R-Value Observed: 0.192 (Depositor) 
Space Group: F 41 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 186.299α = 90
b = 186.299β = 90
c = 186.299γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted 3PGClick on this verticalbar to view detailsBest fitted 3PYClick on this verticalbar to view detailsBest fitted PO4Click on this verticalbar to view details

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-06-20
    Type: Initial release
  • Version 1.1: 2023-11-22
    Changes: Data collection, Database references, Refinement description