3KEW

Crystal structure of probable alanyl-trna-synthase from Clostridium perfringens

• PDB DOI: https://doi.org/10.2210/pdb3KEW/pdb

• Classification: TRANSFERASE
• Organism(s): Clostridium perfringens ATCC 13124
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-10-26 Released: 2009-11-03 
• Deposition Author(s): Patskovsky, Y., Toro, R., Gilmore, M., Miller, S., Sauder, J.M., Almo, S.C., Burley, S.K., New York SGX Research Center for Structural Genomics (NYSGXRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.259 
• R-Value Work: 0.219 
• R-Value Observed: 0.220 

Literature

Crystal structure of alanyl-trna-synthase from Clostridium perfringens

Patskovsky, Y., Toro, R., Gilmore, M., Miller, S., Sauder, J.M., Burley, S.K., Almo, S.C.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 55.85 kDa 
• Atom Count: 3,910 
• Modelled Residue Count: 458 
• Deposited Residue Count: 482 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DHHA1 domain protein	A, B	241	Clostridium perfringens ATCC 13124	Mutation(s): 0  Gene Names: ALAS, CPF_0714
UniProt
Find proteins for A0A0H2YPJ4 (Clostridium perfringens (strain ATCC 13124 / DSM 756 / JCM 1290 / NCIMB 6125 / NCTC 8237 / Type A)) Explore A0A0H2YPJ4  Go to UniProtKB:  A0A0H2YPJ4

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.259 
• R-Value Work: 0.219 
• R-Value Observed: 0.220 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.849	α = 90
b = 57.922	β = 90
c = 178.441	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-11-03 
Deposition Author(s): Patskovsky, Y., Toro, R., Gilmore, M., Miller, S., Sauder, J.M., Almo, S.C., Burley, S.K., New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History  

• Version 1.0: 2009-11-03
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Source and taxonomy, Version format compliance
• Version 1.2: 2018-11-21
  Changes: Data collection, Structure summary
• Version 1.3: 2021-02-10
  Changes: Database references, Derived calculations, Structure summary
• Version 1.4: 2024-02-21
  Changes: Data collection, Database references