4HCD | pdb_00004hcd

Crystal structure of D-glucarate dehydratase from agrobacterium tumefaciens complexed with magnesium

• PDB DOI: https://doi.org/10.2210/pdb4HCD/pdb

• Classification: ISOMERASE
• Organism(s): Agrobacterium fabrum str. C58
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2012-09-29 Released: 2013-10-30 
• Deposition Author(s): Fedorov, A.A., Fedorov, E.V., Sakai, A., Millikin, C., Gerlt, J.A., Almo, S.C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.185 (Depositor), 0.183 (DCC) 
• R-Value Work: 
  0.153 (Depositor), 0.151 (DCC) 
• R-Value Observed: 
  0.155 (Depositor) 

Literature

Crystal structure of D-glucarate dehydratase from agrobacterium tumefaciens complexed with magnesium

Fedorov, A.A., Fedorov, E.V., Sakai, A., Millikin, C., 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: Dihedral - D4  (Explore in 3D)
Global Stoichiometry: Homo 8-mer - A8 

Biological assembly 2 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 45.96 kDa 
• Atom Count: 3,647 
• Modeled Residue Count: 384 
• Deposited Residue Count: 402 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Isomerase/lactonizing enzyme	A	402	Agrobacterium fabrum str. C58	Mutation(s): 0  Gene Names: Atu3453
UniProt
Find proteins for Q7CSI0 (Agrobacterium fabrum (strain C58 / ATCC 33970)) Explore Q7CSI0  Go to UniProtKB:  Q7CSI0

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CL	B [auth A], C [auth A], D [auth A], E [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG	F [auth A], G [auth A], H [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N
NA	I [auth A], J [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.185 (Depositor), 0.183 (DCC) 
• R-Value Work:  0.153 (Depositor), 0.151 (DCC) 
• R-Value Observed: 0.155 (Depositor) 

Space Group: I 4 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 118.733	α = 90
b = 118.733	β = 90
c = 133.199	γ = 90

Software Package:

Software Name	Purpose
MAR345dtb	data collection
PHENIX	model building
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-10-30 
Deposition Author(s): Fedorov, A.A., Fedorov, E.V., Sakai, A., Millikin, C., Gerlt, J.A., Almo, S.C.

Revision History  

• Version 1.0: 2013-10-30
  Type: Initial release
  
• Version 1.1: 2024-11-20
  Changes: Data collection, Database references, Derived calculations, Structure summary