2I9U | pdb_00002i9u

Crystal Structure of Guanine Deaminase from C. acetobutylicum with bound guanine in the active site

• PDB DOI: https://doi.org/10.2210/pdb2I9U/pdb

• Classification: HYDROLASE
• Organism(s): Clostridium acetobutylicum ATCC 824
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2006-09-06 Released: 2006-09-19 
• Deposition Author(s): Kumaran, D., Burley, S.K., Swaminathan, S., New York SGX Research Center for Structural Genomics (NYSGXRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free: 
  0.224 (Depositor), 0.224 (DCC) 
• R-Value Work: 
  0.194 (Depositor), 0.194 (DCC) 
• R-Value Observed: 
  0.194 (Depositor) 

Literature

Crystal Structure of Guanine Deaminase from C. acetobutylicum with bound guanine in the active site

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

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)

Macromolecule Content 

• Total Structure Weight: 100.39 kDa 
• Atom Count: 7,136 
• Modeled Residue Count: 838 
• Deposited Residue Count: 878 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytosine/guanine deaminase related protein	A, B	439	Clostridium acetobutylicum ATCC 824	Mutation(s): 0  EC: 3.5.4.3
UniProt
Find proteins for Q97MB6 (Clostridium acetobutylicum (strain ATCC 824 / DSM 792 / JCM 1419 / IAM 19013 / LMG 5710 / NBRC 13948 / NRRL B-527 / VKM B-1787 / 2291 / W)) Explore Q97MB6  Go to UniProtKB:  Q97MB6

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GUN	D [auth A], G [auth B]	GUANINE C5 H5 N5 O UYTPUPDQBNUYGX-UHFFFAOYSA-N
GOL	E [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
FE	C [auth A], F [auth B]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free:  0.224 (Depositor), 0.224 (DCC) 
• R-Value Work:  0.194 (Depositor), 0.194 (DCC) 
• R-Value Observed: 0.194 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 87.385	α = 90
b = 88.994	β = 90
c = 139.596	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-09-19 
Deposition Author(s): Kumaran, D., Burley, S.K., Swaminathan, S., New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History  

• Version 1.0: 2006-09-19
  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: 2024-02-21
  Changes: Data collection, Database references