4KPL

Crystal structure of d-mannonate dehydratase from chromohalobacter salexigens complexed with Mg,d-mannonate and 2-keto-3-deoxy-d-gluconate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.173 
  • R-Value Observed: 0.175 

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Crystal structure of d-mannonate dehydratase from chromohalobacter salexigens complexed with Mg,d-mannonate and 2-keto-3-deoxy-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 salexigens DSM 3043Mutation(s): 0 
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 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CS2
Query on CS2

Download Ideal Coordinates CCD File 
I [auth A],
L [auth B],
T [auth E],
V [auth F]
D-MANNONIC ACID
C6 H12 O7
RGHNJXZEOKUKBD-MBMOQRBOSA-N
KDG
Query on KDG

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BA [auth H],
N [auth C],
Q [auth D],
Y [auth G]
2-KETO-3-DEOXYGLUCONATE
C6 H10 O6
WPAMZTWLKIDIOP-WVZVXSGGSA-N
GOL
Query on GOL

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Z [auth G]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
CL
Query on CL

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J [auth A],
O [auth C],
R [auth D],
W [auth F]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG
Query on MG

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AA [auth G]
CA [auth H]
K [auth A]
M [auth B]
P [auth C]
AA [auth G],
CA [auth H],
K [auth A],
M [auth B],
P [auth C],
S [auth D],
U [auth E],
X [auth F]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.173 
  • R-Value Observed: 0.175 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 110.242α = 90
b = 167.263β = 90
c = 168.863γ = 90
Software Package:
Software NamePurpose
CBASSdata collection
BALBESphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-05-14
    Type: Initial release
  • Version 1.1: 2023-09-20
    Changes: Data collection, Database references, Derived calculations, Refinement description