3CJP | pdb_00003cjp

Crystal structure of an uncharacterized amidohydrolase CAC3332 from Clostridium acetobutylicum

• PDB DOI: https://doi.org/10.2210/pdb3CJP/pdb

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


• Deposited: 2008-03-13 Released: 2008-03-25 
• Deposition Author(s): Malashkevich, V.N., Toro, R., Ramagopal, U.A., Bonanno, J.B., Meyer, A., Sauder, J.M., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 
  0.241 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.184 (Depositor), 0.185 (DCC) 
• R-Value Observed: 
  0.187 (Depositor) 

Literature

Crystal structure of an uncharacterized amidohydrolase CAC3332 from Clostridium acetobutylicum.

Malashkevich, V.N., Toro, R., Ramagopal, U.A., Bonanno, J.B., Meyer, A., 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 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 60.87 kDa 
• Atom Count: 4,436 
• Modeled Residue Count: 524 
• Deposited Residue Count: 544 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Predicted amidohydrolase, dihydroorotase family	A, B	272	Clostridium acetobutylicum ATCC 824	Mutation(s): 0  Gene Names: CA_C3337
UniProt
Find proteins for Q97DY3 (Clostridium acetobutylicum (strain ATCC 824 / DSM 792 / JCM 1419 / IAM 19013 / LMG 5710 / NBRC 13948 / NRRL B-527 / VKM B-1787 / 2291 / W)) Explore Q97DY3  Go to UniProtKB:  Q97DY3

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free:  0.241 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.184 (Depositor), 0.185 (DCC) 
• R-Value Observed: 0.187 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.628	α = 90
b = 77.273	β = 96.09
c = 72.661	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
SHELX	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
CBASS	data collection
HKL-2000	data reduction
SHELXD	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-03-25 
Deposition Author(s): Malashkevich, V.N., Toro, R., Ramagopal, U.A., Bonanno, J.B., Meyer, A., Sauder, J.M., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History  

• Version 1.0: 2008-03-25
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Refinement description, Version format compliance
• Version 1.2: 2017-10-25
  Changes: Refinement description
• Version 1.3: 2018-11-14
  Changes: Data collection, Structure summary
• Version 1.4: 2021-02-03
  Changes: Database references, Derived calculations, Structure summary
• Version 1.5: 2024-02-21
  Changes: Data collection, Database references