3HM7 | pdb_00003hm7

Crystal structure of allantoinase from Bacillus halodurans C-125

• PDB DOI: https://doi.org/10.2210/pdb3HM7/pdb

• Classification: HYDROLASE
• Organism(s): Halalkalibacterium halodurans
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-05-28 Released: 2009-06-09 
• Deposition Author(s): Patskovsky, Y., Romero, R., Rutter, M., Miller, S., Wasserman, S.R., Sauder, J.M., Raushel, F.M., Burley, S.K., Almo, S.C., New York Structural GenomiX Research Consortium (NYSGXRC), New York SGX Research Center for Structural Genomics (NYSGXRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 
  0.267 (Depositor), 0.267 (DCC) 
• R-Value Work: 
  0.240 (Depositor), 0.240 (DCC) 
• R-Value Observed: 
  0.241 (Depositor) 

Literature

Crystal Structure of Allantoinase from Bacillus Halodurans

Patskovsky, Y., Romero, R., Rutter, M., Miller, S., Raushel, F.M., Wasserman, S.R., Sauder, J.M., Burley, S.K., 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 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)

Biological Assembly 3  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 3 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 299.3 kDa 
• Atom Count: 20,901 
• Modeled Residue Count: 2,616 
• Deposited Residue Count: 2,688 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Allantoinase	A, B, C, D, E, F	448	Halalkalibacterium halodurans	Mutation(s): 0  Gene Names: allB, pucH, BH2309 EC: 3.5.2.5
UniProt
Find proteins for Q9KAH8 (Halalkalibacterium halodurans (strain ATCC BAA-125 / DSM 18197 / FERM 7344 / JCM 9153 / C-125)) Explore Q9KAH8  Go to UniProtKB:  Q9KAH8

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	G [auth A], H [auth B], I [auth C], J [auth D], K [auth E], L [auth F]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free:  0.267 (Depositor), 0.267 (DCC) 
• R-Value Work:  0.240 (Depositor), 0.240 (DCC) 
• R-Value Observed: 0.241 (Depositor) 

Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 157.658	α = 90
b = 157.658	β = 90
c = 418.026	γ = 120

Software Package:

Software Name	Purpose
SHELXD	phasing
RESOLVE	model building
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
RESOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-06-09 
Deposition Author(s): Patskovsky, Y., Romero, R., Rutter, M., Miller, S., Wasserman, S.R., Sauder, J.M., Raushel, F.M., Burley, S.K., Almo, S.C., New York Structural GenomiX Research Consortium (NYSGXRC), New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History  

• Version 1.0: 2009-06-09
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Refinement description, Version format compliance
• Version 1.2: 2018-01-24
  Changes: Structure summary
• Version 1.3: 2018-11-21
  Changes: Data collection, Structure summary
• Version 1.4: 2021-02-10
  Changes: Database references, Derived calculations, Structure summary
• Version 1.5: 2024-02-21
  Changes: Data collection, Database references