3QKE

Crystal structure of D-mannonate dehydratase from Chromohalobacter Salexigens complexed with Mg and D-Gluconate

• PDB DOI:  https://doi.org/10.2210/pdb3QKE/pdb

• Classification: ISOMERASE
• Organism(s): Chromohalobacter salexigens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2011-02-01 Released: 2012-02-01 
• Deposition Author(s): Fedorov, A.A., Fedorov, E.V., Wichelecki, D., Gerlt, J.A., Almo, S.C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free: 0.211 
• R-Value Work: 0.179 
• R-Value Observed: 0.181 

Literature

Cystal structure 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.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global 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)

Biological Assembly 3  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 3 assigned by authors and generated by PISA (software)

Biological Assembly 4  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 4 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 365.51 kDa 
• Atom Count: 27,932 
• Modelled Residue Count: 3,174 
• Deposited Residue Count: 3,240 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mandelate racemase/muconate lactonizing enzyme	A, B, C, D, E, F, G, H	405	Chromohalobacter salexigens	Mutation(s): 0  Gene Names: Csal_2974 EC: 4.2.1 (UniProt), 4.2.1.39 (UniProt), 4.2.1.8 (UniProt)
UniProt
Find proteins for Q1QT89 (Chromohalobacter salexigens (strain ATCC BAA-138 / DSM 3043 / CIP 106854 / NCIMB 13768 / 1H11)) Explore Q1QT89  Go to UniProtKB:  Q1QT89

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GCO	I [auth A], K [auth B], M [auth C], O [auth D], Q [auth E], S [auth F], U [auth G], W [auth H]	D-gluconic acid C6 H12 O7 RGHNJXZEOKUKBD-SQOUGZDYSA-N
MG	J [auth A], L [auth B], N [auth C], P [auth D], R [auth E], T [auth F], V [auth G], X [auth H]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free: 0.211 
• R-Value Work: 0.179 
• R-Value Observed: 0.181 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 195.536	α = 90
b = 85.782	β = 110.33
c = 195.143	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
BALBES	phasing
PHENIX	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-02-01 
Deposition Author(s): Fedorov, A.A., Fedorov, E.V., Wichelecki, D., Gerlt, J.A., Almo, S.C.

Revision History  

• Version 1.0: 2012-02-01
  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: 2023-09-13
  Changes: Data collection, Database references, Refinement description, Structure summary