3OOO | pdb_00003ooo

The structure of a proline dipeptidase from Streptococcus agalactiae 2603V

PDB DOI: https://doi.org/10.2210/pdb3OOO/pdb

Classification: HYDROLASE
Organism(s): Streptococcus agalactiae 2603V/R
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2010-08-31 Released: 2010-09-22
Deposition Author(s): Fan, Y., Wu, R., Morales, J., Clancy, S., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.57 Å
R-Value Free:
0.215 (Depositor), 0.219 (DCC)
R-Value Work:
0.186 (Depositor), 0.191 (DCC)
R-Value Observed:
0.188 (Depositor)

wwPDB Validation 3D Report Full Report

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This is version 1.3 of the entry. See complete history.

Literature

The structure of a proline dipeptidase from Streptococcus agalactiae 2603V

Fan, Y., Wu, R., Morales, J., Clancy, S., Joachimiak, A.

To be published.

Macromolecule Content

Total Structure Weight: 30.79 kDa
Atom Count: 2,641
Modeled Residue Count: 264
Deposited Residue Count: 264
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Proline dipeptidase	A, B	132	Streptococcus agalactiae 2603V/R	Mutation(s): 0 Gene Names: pepQ, SAG0706
UniProt
Find proteins for Q8E0M4 (Streptococcus agalactiae serotype V (strain ATCC BAA-611 / 2603 V/R)) Explore Q8E0M4 Go to UniProtKB: Q8E0M4
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8E0M4
Sequence Annotations Expand
Reference Sequence

Small Molecules

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.57 Å
R-Value Free: 0.215 (Depositor), 0.219 (DCC)
R-Value Work: 0.186 (Depositor), 0.191 (DCC)
R-Value Observed: 0.188 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.744	α = 90
b = 58.325	β = 90
c = 101.995	γ = 90

Software Package:

Software Name	Purpose
SBC-Collect	data collection
SHELXD	phasing
MLPHARE	phasing
ARP	model building
WARP	model building
HKL-3000	phasing
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling

Structure Validation

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Entry History

Deposition Data

Released Date: 2010-09-22

Deposition Author(s):

Midwest Center for Structural Genomics (MCSG)

Revision History (Full details and data files)

Version 1.0: 2010-09-22
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2017-11-08
Changes: Refinement description
Version 1.3: 2024-11-06
Changes: Data collection, Database references, Derived calculations, Structure summary

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), 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 R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.