4F4R | pdb_00004f4r

Crystal structure of D-mannonate dehydratase homolog from Chromohalobacter salexigens (Target EFI-502114), with bound NA, ordered loop

• PDB DOI: https://doi.org/10.2210/pdb4F4R/pdb

• Classification: LYASE
• Organism(s): Chromohalobacter israelensis DSM 3043
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2012-05-11 Released: 2012-06-27 
• Deposition Author(s): Vetting, M.W., Toro, R., Bhosle, R., Al Obaidi, N.F., Morisco, L.L., Wasserman, S.R., Sojitra, S., Washington, E., Scott Glenn, A., Chowdhury, S., Evans, B., Hammonds, J., Hillerich, B., Love, J., Seidel, R.D., Imker, H.J., Gerlt, J.A., Almo, S.C., Enzyme Function Initiative (EFI), Medical Structural Genomics of Pathogenic Protozoa (MSGPP)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.171 (Depositor), 0.168 (DCC) 
• R-Value Work: 
  0.145 (Depositor), 0.144 (DCC) 
• R-Value Observed: 
  0.146 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of D-mannonate dehydratase homolog from Chromohalobacter salexigens (Target EFI-502114), with bound NA, ordered loop

Vetting, M.W., Toro, R., Bhosle, R., Al Obaidi, N.F., Morisco, L.L., Wasserman, S.R., Sojitra, S., Washington, E., Scott Glenn, A., Chowdhury, S., Evans, B., Hammonds, J., Hillerich, B., Love, J., Seidel, R.D., Imker, H.J., Gerlt, J.A., Almo, S.C., Enzyme Function Initiative (EFI)

To be published.

Biological Assembly 1  

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

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 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 48.2 kDa 
• Atom Count: 3,658 
• Modeled Residue Count: 408 
• Deposited Residue Count: 426 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
D-mannonate dehydratase	A	426	Chromohalobacter israelensis DSM 3043	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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	D [auth A], E [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CL	C [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA	B [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.171 (Depositor), 0.168 (DCC) 
• R-Value Work:  0.145 (Depositor), 0.144 (DCC) 
• R-Value Observed: 0.146 (Depositor) 

Space Group: P 4 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 111.389	α = 90
b = 111.389	β = 90
c = 84.576	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
MOSFLM	data reduction
SCALA	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-06-27 
Deposition Author(s): Vetting, M.W., Toro, R., Bhosle, R., Al Obaidi, N.F., Morisco, L.L., Wasserman, S.R., Sojitra, S., Washington, E., Scott Glenn, A., Chowdhury, S., Evans, B., Hammonds, J., Hillerich, B., Love, J., Seidel, R.D., Imker, H.J., Gerlt, J.A., Almo, S.C., Enzyme Function Initiative (EFI), Medical Structural Genomics of Pathogenic Protozoa (MSGPP)

Revision History  

• Version 1.0: 2012-06-27
  Type: Initial release
  
• Version 1.1: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description