3OVK

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)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.239
R-Value Work: 0.176
R-Value Observed: 0.180

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

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.

Macromolecule Content

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

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

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
UniProt
Find proteins for Q48RL4 (Streptococcus pyogenes serotype M28 (strain MGAS6180)) Explore Q48RL4 Go to UniProtKB: Q48RL4
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q48RL4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on 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
R-Value Work: 0.176
R-Value Observed: 0.180
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

View Full Validation Report

Entry History

Deposition Data

Released Date: 2010-11-03

Deposition Author(s):

Midwest Center for Structural Genomics (MCSG)

Revision History (Full details and data files)

Version 1.0: 2010-11-03
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.