3SMV | pdb_00003smv

X-ray Crystal Structure of L-Azetidine-2-Carboxylate Hydrolase

• PDB DOI: https://doi.org/10.2210/pdb3SMV/pdb

• Classification: HYDROLASE
• Organism(s): Pseudomonas sp. A2C
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2011-06-28 Released: 2012-07-18 
• Deposition Author(s): Toyoda, M., Mikami, B., Jitsumori, K., Wackett, L.P., Esaki, N., Kurihara, T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.38 Å
• R-Value Free: 
  0.158 (Depositor), 0.154 (DCC) 
• R-Value Work: 
  0.122 (Depositor), 0.117 (DCC) 
• R-Value Observed: 
  0.123 (Depositor) 

Literature

Crystal structure of L-Azetidine-2-carboxylate hydrolase from Pseudomonas sp. strain A2C

Jitsumori, K., Toyoda, M., Mikami, B., Wackett, L.P., Kurihara, T., Esaki, N.

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)

Macromolecule Content 

• Total Structure Weight: 28.04 kDa 
• Atom Count: 2,531 
• Modeled Residue Count: 233 
• Deposited Residue Count: 240 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
(S)-2-haloacid dehalogenase	A	240	Pseudomonas sp. A2C	Mutation(s): 0  EC: 3.8.1.2 (PDB Primary Data), 3.5 (UniProt)
UniProt
Find proteins for B2Z3V8 (Pseudomonas sp. (strain A2C)) Explore B2Z3V8  Go to UniProtKB:  B2Z3V8

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	B [auth A], C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
IMD	K [auth A]	IMIDAZOLE C3 H5 N2 RAXXELZNTBOGNW-UHFFFAOYSA-O

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.38 Å
• R-Value Free:  0.158 (Depositor), 0.154 (DCC) 
• R-Value Work:  0.122 (Depositor), 0.117 (DCC) 
• R-Value Observed: 0.123 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 35.612	α = 90
b = 63.588	β = 105.54
c = 54.665	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHENIX	model building
PHENIX	refinement
DENZO	data reduction
SCALEPACK	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-07-18 
Deposition Author(s): Toyoda, M., Mikami, B., Jitsumori, K., Wackett, L.P., Esaki, N., Kurihara, T.

Revision History  

• Version 1.0: 2012-07-18
  Type: Initial release
  
• Version 1.1: 2024-03-20
  Changes: Data collection, Database references, Derived calculations
• Version 1.2: 2024-05-01
  Changes: Advisory, Source and taxonomy, Structure summary
• Version 1.3: 2024-06-12
  Changes: Source and taxonomy