1V72 | pdb_00001v72

Crystal Structure of Phenylserine Aldolase from Pseudomonas Putida

• PDB DOI: https://doi.org/10.2210/pdb1V72/pdb

• Classification: LYASE
• Organism(s): Pseudomonas putida
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2003-12-09 Released: 2005-03-01 
• Deposition Author(s): Omi, R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free: 
  0.236 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.217 (Depositor), 0.217 (DCC) 
• R-Value Observed: 
  0.217 (Depositor) 

Literature

Crystal Structure of Phenylserine Aldolase from Pseudomonas Putida

Omi, R., Miyahara, I., Misono, H., Hirotsu, K.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Macromolecule Content 

• Total Structure Weight: 38.54 kDa 
• Atom Count: 2,802 
• Modeled Residue Count: 345 
• Deposited Residue Count: 356 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Aldolase	A	356	Pseudomonas putida	Mutation(s): 0  EC: 4.1.2.26 (PDB Primary Data), 4.1.2.48 (UniProt)
UniProt
Find proteins for Q59IT3 (Pseudomonas putida) Explore Q59IT3  Go to UniProtKB:  Q59IT3

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PLP	C [auth A]	PYRIDOXAL-5'-PHOSPHATE C8 H10 N O6 P NGVDGCNFYWLIFO-UHFFFAOYSA-N
ZN	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free:  0.236 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.217 (Depositor), 0.217 (DCC) 
• R-Value Observed: 0.217 (Depositor) 

Space Group: P 4₂ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 95.489	α = 90
b = 95.489	β = 90
c = 107.115	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
SCALEPACK	data scaling
AMoRE	phasing
CNS	refinement
HKL-2000	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-03-01 
Deposition Author(s): Omi, R.

Revision History  

• Version 1.0: 2005-03-01
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Version format compliance
• Version 1.3: 2023-12-27
  Changes: Data collection, Database references, Derived calculations