2GOK | pdb_00002gok

Crystal structure of the imidazolonepropionase from Agrobacterium tumefaciens at 1.87 A resolution

• PDB DOI: https://doi.org/10.2210/pdb2GOK/pdb

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


• Deposited: 2006-04-13 Released: 2006-04-25 
• Deposition Author(s): Tyagi, R., Kumaran, D., Swaminathan, S., Burley, S.K., New York SGX Research Center for Structural Genomics (NYSGXRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.87 Å
• R-Value Free: 
  0.231 (Depositor), 0.231 (DCC) 
• R-Value Work: 
  0.207 (Depositor), 0.206 (DCC) 
• R-Value Observed: 
  0.207 (Depositor) 

Literature

X-ray structure of imidazolonepropionase from Agrobacterium tumefaciens at 1.87 A resolution.

Tyagi, R., Kumaran, D., Burley, S.K., Swaminathan, S.

(2007) Proteins 69: 652-658

• PubMed: 17640072 
• DOI: https://doi.org/10.1002/prot.21559
• Primary Citation Related Structures: 
  2GOK, 2PUZ

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Organizational Affiliation: 
• Biology Department, Brookhaven National Laboratory, Upton, New York 11973, USA.

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)

Macromolecule Content 

• Total Structure Weight: 91.61 kDa 
• Atom Count: 6,549 
• Modeled Residue Count: 808 
• Deposited Residue Count: 858 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Imidazolonepropionase	A, B	429	Agrobacterium fabrum str. C58	Mutation(s): 0  Gene Names: hutI EC: 3.5.2.7
UniProt
Find proteins for Q8U8Z6 (Agrobacterium fabrum (strain C58 / ATCC 33970)) Explore Q8U8Z6  Go to UniProtKB:  Q8U8Z6

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	H [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
FE	C [auth A], E [auth B]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N
CL	G [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG	D [auth A], F [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.87 Å
• R-Value Free:  0.231 (Depositor), 0.231 (DCC) 
• R-Value Work:  0.207 (Depositor), 0.206 (DCC) 
• R-Value Observed: 0.207 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 140.754	α = 90
b = 63.63	β = 111.93
c = 103.716	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
CBASS	data collection
HKL-2000	data scaling
SHELXD	phasing
SHARP	phasing
ARP/wARP	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-04-25 
Deposition Author(s): Tyagi, R., Kumaran, D., Swaminathan, S., Burley, S.K., New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History  

• Version 1.0: 2006-04-25
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Source and taxonomy, Version format compliance
• Version 1.3: 2021-02-03
  Changes: Database references, Derived calculations, Structure summary
• Version 1.4: 2024-02-14
  Changes: Data collection, Database references