4K2S

Crystal structure of the mutant P317A of d-mannonate dehydratase from chromohalobacter salexigens complexed with mg and d-gluconate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.169 
  • R-Value Observed: 0.170 

Starting Model: experimental
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This is version 2.1 of the entry. See complete history


Literature

Crystal structure of the mutant P317A of d-mannonate dehydratase from chromohalobacter salexigens complexed with mg and d-gluconate

Fedorov, A.A.Fedorov, E.V.Wichelecki, D.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
D-mannonate dehydratase
A, B, C, D, E
A, B, C, D, E, F, G, H
405Chromohalobacter israelensis DSM 3043Mutation(s): 1 
Gene Names: Csal_2974
EC: 4.2.1.8
UniProt
Find proteins for Q1QT89 (Chromohalobacter salexigens (strain ATCC BAA-138 / DSM 3043 / CIP 106854 / NCIMB 13768 / 1H11))
Explore Q1QT89 
Go to UniProtKB:  Q1QT89
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ1QT89
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GCO
Query on GCO

Download Ideal Coordinates CCD File 
BA [auth F]
FA [auth G]
I [auth A]
IA [auth H]
L [auth B]
BA [auth F],
FA [auth G],
I [auth A],
IA [auth H],
L [auth B],
O [auth C],
S [auth D],
W [auth E]
D-gluconic acid
C6 H12 O7
RGHNJXZEOKUKBD-SQOUGZDYSA-N
GOL
Query on GOL

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R [auth C]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
CL
Query on CL

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AA [auth E]
DA [auth F]
EA [auth F]
K [auth A]
V [auth D]
AA [auth E],
DA [auth F],
EA [auth F],
K [auth A],
V [auth D],
Z [auth E]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG
Query on MG

Download Ideal Coordinates CCD File 
CA [auth F]
GA [auth G]
HA [auth G]
J [auth A]
JA [auth H]
CA [auth F],
GA [auth G],
HA [auth G],
J [auth A],
JA [auth H],
M [auth B],
N [auth B],
P [auth C],
Q [auth C],
T [auth D],
U [auth D],
X [auth E],
Y [auth E]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.169 
  • R-Value Observed: 0.170 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 196.334α = 90
b = 85.79β = 110.47
c = 195.638γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-04-09
    Type: Initial release
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Database references, Derived calculations, Structure summary
  • Version 2.1: 2023-09-20
    Changes: Data collection, Database references, Refinement description, Structure summary