4GME

Crystal structure of mannonate dehydratase (target EFI-502209) from caulobacter crescentus cb15 complexed with magnesium and d-mannonate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.196 
  • R-Value Work: 0.156 
  • R-Value Observed: 0.157 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Crystal Structure of Mannonate Dehydratase from Caulobacter Crescentus Cb15

Patskovsky, Y.Toro, R.Bhosle, R.Hillerich, B.Seidel, R.D.Washington, E.Scott Glenn, A.Chowdhury, S.Evans, B.Hammonds, J.Zencheck, W.D.Imker, H.J.Gerlt, J.A.Almo, S.C.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Mandelate racemase/muconate lactonizing enzyme familyA,
B [auth C]
426Caulobacter vibrioides CB15Mutation(s): 0 
Gene Names: CC_0532
UniProt
Find proteins for Q9AAR4 (Caulobacter vibrioides (strain ATCC 19089 / CIP 103742 / CB 15))
Explore Q9AAR4 
Go to UniProtKB:  Q9AAR4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9AAR4
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CS2
Query on CS2

Download Ideal Coordinates CCD File 
I [auth C]D-MANNONIC ACID
C6 H12 O7
RGHNJXZEOKUKBD-MBMOQRBOSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
E [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
CO3
Query on CO3

Download Ideal Coordinates CCD File 
F [auth A]CARBONATE ION
C O3
BVKZGUZCCUSVTD-UHFFFAOYSA-L
CL
Query on CL

Download Ideal Coordinates CCD File 
D [auth A],
H [auth C]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG
Query on MG

Download Ideal Coordinates CCD File 
C [auth A],
G [auth C]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.196 
  • R-Value Work: 0.156 
  • R-Value Observed: 0.157 
  • Space Group: I 4
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 115.801α = 90
b = 115.801β = 90
c = 118.131γ = 90
Software Package:
Software NamePurpose
PHASERphasing
REFMACrefinement
HKL-3000data reduction
HKL-3000data scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2012-09-12
    Type: Initial release
  • Version 1.1: 2023-09-13
    Changes: Data collection, Database references, Derived calculations, Refinement description