3RGT | pdb_00003rgt

Crystal structure of d-mannonate dehydratase from Chromohalobacter salexigens complexed with D-Arabinohydroxamate

• PDB DOI: https://doi.org/10.2210/pdb3RGT/pdb

• Classification: LYASE
• Organism(s): Chromohalobacter israelensis
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2011-04-09 Released: 2012-04-11 
• 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: 1.90 Å
• R-Value Free: 
  0.222 (Depositor), 0.214 (DCC) 
• R-Value Work: 
  0.178 (Depositor), 0.172 (DCC) 
• R-Value Observed: 
  0.180 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of d-mannonate dehydratase from Chromohalobacter salexigens complexed with d-arabinohydroxamate

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

Biological assembly 3 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 182.83 kDa 
• Atom Count: 13,254 
• Modeled Residue Count: 1,546 
• Deposited Residue Count: 1,620 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
D-mannonate dehydratase	A, B, C, D	405	Chromohalobacter israelensis	Mutation(s): 0  Gene Names: Csal_2974 EC: 4.2.1.8 (PDB Primary Data), 4.2.1 (UniProt), 4.2.1.39 (UniProt)
UniProt
Find proteins for Q1QT89 (Chromohalobacter israelensis (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
EZ4	F [auth A], H [auth B], J [auth C], L [auth D]	(2S,3R,4R)-2,3,4,5-tetrahydroxy-N-oxo-pentanamide C5 H9 N O6 VIMQVNVKLDVNFU-JJYYJPOSSA-N
CO	E [auth A], G [auth B], I [auth C], K [auth D]	COBALT (II) ION Co XLJKHNWPARRRJB-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.222 (Depositor), 0.214 (DCC) 
• R-Value Work:  0.178 (Depositor), 0.172 (DCC) 
• R-Value Observed: 0.180 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 110.712	α = 90
b = 179.657	β = 90
c = 85.422	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: 2012-04-11 
Deposition Author(s): Fedorov, A.A., Fedorov, E.V., Wichelecki, D., Gerlt, J.A., Almo, S.C.

Revision History  

• Version 1.0: 2012-04-11
  Type: Initial release
  
• Version 1.1: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description