4GME | pdb_00004gme

Crystal structure of mannonate dehydratase (target EFI-502209) from caulobacter crescentus cb15 complexed with magnesium and d-mannonate

• PDB DOI: https://doi.org/10.2210/pdb4GME/pdb

• Classification: LYASE
• Organism(s): Caulobacter vibrioides CB15
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2012-08-15 Released: 2012-09-12 
• Deposition Author(s): Patskovsky, Y., Toro, R., Bhosle, R., Hillerich, B., Seidel, R.D., Washington, E., Scott Glenn, A., Chowdhury, S., Evans, B., Hammonds, J., Zencheck, W.D., Imker, H.J., Gerlt, J.A., Almo, S.C., Enzyme Function Initiative (EFI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.196 (Depositor), 0.197 (DCC) 
• R-Value Work: 
  0.156 (Depositor), 0.157 (DCC) 
• R-Value Observed: 
  0.157 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of Mannonate Dehydratase from Caulobacter Crescentus Cb15

Patskovsky, Y., Toro, R., Bhosle, R., Hillerich, B., Seidel, R.D., Washington, E., Scott Glenn, A., Chowdhury, S., Evans, B., Hammonds, J., Zencheck, W.D., Imker, H.J., Gerlt, J.A., Almo, S.C.

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)

Macromolecule Content 

• Total Structure Weight: 95.41 kDa 
• Atom Count: 6,886 
• Modeled Residue Count: 806 
• Deposited Residue Count: 852 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mandelate racemase/muconate lactonizing enzyme family	A, B [auth C]	426	Caulobacter vibrioides CB15	Mutation(s): 0  Gene Names: CC_0532 EC: 4.2.1.8
UniProt
Find proteins for Q9AAR4 (Caulobacter vibrioides (strain ATCC 19089 / CIP 103742 / CB 15)) Explore Q9AAR4  Go to UniProtKB:  Q9AAR4

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CS2	I [auth C]	D-MANNONIC ACID C6 H12 O7 RGHNJXZEOKUKBD-MBMOQRBOSA-N
GOL	E [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CO3	F [auth A]	CARBONATE ION C O3 BVKZGUZCCUSVTD-UHFFFAOYSA-L
CL	D [auth A], H [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG	C [auth A], G [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.196 (Depositor), 0.197 (DCC) 
• R-Value Work:  0.156 (Depositor), 0.157 (DCC) 
• R-Value Observed: 0.157 (Depositor) 

Space Group: I 4

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 115.801	α = 90
b = 115.801	β = 90
c = 118.131	γ = 90

Software Package:

Software Name	Purpose
PHASER	phasing
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-09-12 
Deposition Author(s): Patskovsky, Y., Toro, R., Bhosle, R., Hillerich, B., Seidel, R.D., Washington, E., Scott Glenn, A., Chowdhury, S., Evans, B., Hammonds, J., Zencheck, W.D., Imker, H.J., Gerlt, J.A., Almo, S.C., Enzyme Function Initiative (EFI)

Revision History  

• Version 1.0: 2012-09-12
  Type: Initial release
  
• Version 1.1: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description