3IL0 | pdb_00003il0

The crystal structure of the aminopeptidase P,XAA-pro aminopeptidase from Streptococcus thermophilus

PDB DOI: https://doi.org/10.2210/pdb3IL0/pdb

Classification: HYDROLASE
Organism(s): Streptococcus thermophilus LMG 18311
Expression System: Escherichia coli BL21
Mutation(s): No

Deposited: 2009-08-06 Released: 2009-09-08
Deposition Author(s): Zhang, R., Hatzos, C., Cobb, G., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free:
0.237 (Depositor), 0.242 (DCC)
R-Value Work:
0.201 (Depositor), 0.210 (DCC)
R-Value Observed:
0.203 (Depositor)

wwPDB Validation 3D Report Full Report

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This is version 1.2 of the entry. See complete history.

Literature

The crystal structure of the aminopeptidase P,XAA-pro aminopeptidase from Streptococcus thermophilus

Zhang, R., Hatzos, C., Cobb, G., Joachimiak, A.

To be published.

Macromolecule Content

Total Structure Weight: 30.59 kDa
Atom Count: 2,178
Modeled Residue Count: 256
Deposited Residue Count: 262
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Aminopeptidase P; XAA-pro aminopeptidase	A, B	131	Streptococcus thermophilus LMG 18311	Mutation(s): 0 Gene Names: GI:55737699, pepP, stu1742
UniProt
Find proteins for Q5M2R3 (Streptococcus thermophilus (strain ATCC BAA-250 / LMG 18311)) Explore Q5M2R3 Go to UniProtKB: Q5M2R3
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q5M2R3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth B]	C [auth A], D [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.237 (Depositor), 0.242 (DCC)
R-Value Work: 0.201 (Depositor), 0.210 (DCC)
R-Value Observed: 0.203 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.303	α = 90
b = 80.396	β = 90
c = 100.858	γ = 90

Software Package:

Software Name	Purpose
SBC-Collect	data collection
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: 2009-09-08

Deposition Author(s):

Midwest Center for Structural Genomics (MCSG)

Revision History (Full details and data files)

Version 1.0: 2009-09-08
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Source and taxonomy, Version format compliance
Version 1.2: 2024-02-21
Changes: Data collection, Database references, Derived calculations

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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.