3AZQ | pdb_00003azq

Crystal structure of puromycin hydrolase S511A mutant complexed with PGG

• PDB DOI: https://doi.org/10.2210/pdb3AZQ/pdb

• Classification: HYDROLASE
• Organism(s): Streptomyces morookaense
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2011-05-27 Released: 2011-07-27 
• Deposition Author(s): Matoba, Y., Sugiyama, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 
  0.240 (Depositor), 0.232 (DCC) 
• R-Value Work: 
  0.193 (Depositor), 0.185 (DCC) 
• R-Value Observed: 
  0.193 (Depositor) 

Starting Model: experimental

Literature

Structural evidence that puromycin hydrolase is a new type of aminopeptidase with a prolyl oligopeptidase family fold

Matoba, Y., Nakayama, A., Oda, K., Noda, M., Kumagai, T., Nishimura, M., Sugiyama, M.

(2011) Proteins 79: 2999-3005

• PubMed: 21905123 
• DOI: https://doi.org/10.1002/prot.23139
• Primary Citation Related Structures: 
  3AZO, 3AZP, 3AZQ

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Organizational Affiliation: 
• Department of Molecular Microbiology and Biotechnology, Graduate School of Biomedical Sciences, Hiroshima University, Minami-ku, Hiroshima, Japan.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 143.96 kDa 
• Atom Count: 10,630 
• Modeled Residue Count: 1,326 
• Deposited Residue Count: 1,330 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Aminopeptidase	A, B	662	Streptomyces morookaense	Mutation(s): 1  Gene Names: pmh
UniProt
Find proteins for Q2HXD9 (Streptomyces morookaense) Explore Q2HXD9  Go to UniProtKB:  Q2HXD9

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
tripeptide PGG	C, D	3	N/A	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth B], L [auth B], M [auth B], N [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free:  0.240 (Depositor), 0.232 (DCC) 
• R-Value Work:  0.193 (Depositor), 0.185 (DCC) 
• R-Value Observed: 0.193 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 84.43	α = 90
b = 142.68	β = 90
c = 156.31	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-07-27 
Deposition Author(s): Matoba, Y., Sugiyama, M.

Revision History  

• Version 1.0: 2011-07-27
  Type: Initial release
  
• Version 1.1: 2011-09-28
  Changes: Database references
• Version 1.2: 2023-11-01
  Changes: Data collection, Database references, Derived calculations, Refinement description