2IJZ | pdb_00002ijz

Crystal structure of aminopeptidase

• PDB DOI: https://doi.org/10.2210/pdb2IJZ/pdb

• Classification: HYDROLASE
• Organism(s): Pseudomonas aeruginosa
• Expression System: Escherichia coli BL21
• Mutation(s): Yes 


• Deposited: 2006-10-02 Released: 2006-11-14 
• Deposition Author(s): Min, T., Burley, S.K., Shapiro, L., New York SGX Research Center for Structural Genomics (NYSGXRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 
  0.291 (Depositor), 0.337 (DCC) 
• R-Value Work: 
  0.255 (Depositor), 0.318 (DCC) 
• R-Value Observed: 
  0.255 (Depositor) 

Starting Model: experimental

Literature

Crystal structrue of putative aminopeptidase 2 from Pseudomonas Aeruginosa

Min, T., Burley, S.K., Shapiro, L.

To be published.

Biological Assembly 1  

Global Symmetry: Tetrahedral - T  (Explore in 3D)
Global Stoichiometry: Homo 12-mer - A12 

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

Macromolecule Content 

• Total Structure Weight: 559.5 kDa 
• Atom Count: 37,617 
• Modeled Residue Count: 4,548 
• Deposited Residue Count: 5,136 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Probable M18-family aminopeptidase 2	A, B, C, D, E, F, G, H, I, J, K, L	428	Pseudomonas aeruginosa	Mutation(s): 1  Gene Names: apeB EC: 3.4.11
UniProt
Find proteins for Q9HYZ3 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)) Explore Q9HYZ3  Go to UniProtKB:  Q9HYZ3

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free:  0.291 (Depositor), 0.337 (DCC) 
• R-Value Work:  0.255 (Depositor), 0.318 (DCC) 
• R-Value Observed: 0.255 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 134.678	α = 60.12
b = 134.553	β = 60.1
c = 134.601	γ = 60.16

Software Package:

Software Name	Purpose
CNS	refinement
CBASS	data collection
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-11-14 
Deposition Author(s): Min, T., Burley, S.K., Shapiro, L., New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History  

• Version 1.0: 2006-11-14
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2021-02-03
  Changes: Database references, Structure summary
• Version 1.4: 2021-10-20
  Changes: Database references
• Version 1.5: 2023-08-30
  Changes: Data collection, Refinement description