3P93

Crystal structure of D-mannonate dehydratase from Chromohalobacter Salexigens complexed with MG,D-Mannonate and 2-keto-3-deoxy-D-Gluconate

• PDB DOI: https://doi.org/10.2210/pdb3P93/pdb

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


• Deposited: 2010-10-15 Released: 2011-10-19 
• Deposition Author(s): Fedorov, A.A., Fedorov, E.V., Wichelecki, D., Gerlt, J.A., Almo, S.C.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.241 
• R-Value Work: 0.199 
• R-Value Observed: 0.201 

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.

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)

Biological Assembly 5  

Global Symmetry: Dihedral - D4  (Explore in 3D)
Global Stoichiometry: Homo 8-mer - A8 

Biological assembly 5 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 365.44 kDa 
• Atom Count: 26,363 
• Modelled Residue Count: 3,077 
• 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
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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CS2	J [auth A], L [auth B], R [auth E], T [auth F]	D-MANNONIC ACID C6 H12 O7 RGHNJXZEOKUKBD-MBMOQRBOSA-N
KDG	N [auth C], P [auth D], V [auth G], X [auth H]	2-KETO-3-DEOXYGLUCONATE C6 H10 O6 WPAMZTWLKIDIOP-WVZVXSGGSA-N
MG	I [auth A], K [auth B], M [auth C], O [auth D], Q [auth E], S [auth F], U [auth G], W [auth H]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.241 
• R-Value Work: 0.199 
• R-Value Observed: 0.201 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 110.242	α = 90
b = 167.263	β = 90
c = 168.863	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: 2011-10-19 
Deposition Author(s): Fedorov, A.A., Fedorov, E.V., Wichelecki, D., Gerlt, J.A., Almo, S.C.

Revision History  

• Version 1.0: 2011-10-19
  Type: Initial release
  
• Version 1.1: 2023-09-06
  Changes: Data collection, Database references, Derived calculations, Refinement description