3OVK | pdb_00003ovk

Crystal structure of an XXA-pro aminopeptidase from Streptococcus pyogenes

• PDB DOI: https://doi.org/10.2210/pdb3OVK/pdb

• Classification: HYDROLASE
• Organism(s): Streptococcus pyogenes M1 GAS
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2010-09-16 Released: 2010-11-03 
• Deposition Author(s): Joachimiak, A., Duke, N.E.C., Volkart, L., Clancy, S., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.239 (Depositor), 0.243 (DCC) 
• R-Value Work: 
  0.176 (Depositor), 0.184 (DCC) 
• R-Value Observed: 
  0.180 (Depositor) 

Literature

Crystal structure of an XXA-pro aminopeptidase from Streptococcus pyogenes

Joachimiak, A., Duke, N.E.C., Volkart, L., Clancy, S., Midwest Center for Structural Genomics (MCSG)

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 4-mer - A4 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 58.81 kDa 
• Atom Count: 4,367 
• Modeled Residue Count: 516 
• Deposited Residue Count: 528 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
AMINOPEPTIDASE P, Xaa-Pro dipeptidase	A, B, C, D	132	Streptococcus pyogenes M1 GAS	Mutation(s): 0  Gene Names: M28_Spy1536, SPY_1824 EC: 3.4.13.9

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B, C, D	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.239 (Depositor), 0.243 (DCC) 
• R-Value Work:  0.176 (Depositor), 0.184 (DCC) 
• R-Value Observed: 0.180 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.086	α = 90
b = 116.991	β = 96.64
c = 49.447	γ = 90

Software Package:

Software Name	Purpose
HKL-3000	data collection
HKL-3000	phasing
MLPHARE	phasing
DM	model building
SHELXD	phasing
RESOLVE	model building
ARP/wARP	model building
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
DM	phasing
RESOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-11-03 
Deposition Author(s): Joachimiak, A., Duke, N.E.C., Volkart, L., Clancy, S., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2010-11-03
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2024-10-16
  Changes: Data collection, Database references, Derived calculations, Structure summary