3I7M | pdb_00003i7m

N-terminal domain of Xaa-Pro dipeptidase from Lactobacillus brevis.

PDB DOI: https://doi.org/10.2210/pdb3I7M/pdb

Classification: HYDROLASE
Organism(s): Levilactobacillus brevis ATCC 367
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2009-07-08 Released: 2009-07-14
Deposition Author(s): Osipiuk, J., Xu, X., Cui, H., Ng, J., Savchenko, A., Edwards, A.M., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.46 Å
R-Value Free:
0.198 (Depositor), 0.203 (DCC)
R-Value Work:
0.163 (Depositor), 0.177 (DCC)
R-Value Observed:
0.164 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 3I7M

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

Literature

X-ray crystal structure of N-terminal domain of Xaa-Pro dipeptidase from Lactobacillus brevis.

Osipiuk, J., Xu, X., Cui, H., Ng, J., Savchenko, A., Edwards, A.M., Joachimiak, A.

To be published.

Macromolecule Content

Total Structure Weight: 16.12 kDa
Atom Count: 1,372
Modeled Residue Count: 134
Deposited Residue Count: 140
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Xaa-Pro dipeptidase	A	140	Levilactobacillus brevis ATCC 367	Mutation(s): 0 Gene Names: LVIS_1204
UniProt
Find proteins for Q03R62 (Levilactobacillus brevis (strain ATCC 367 / BCRC 12310 / CIP 105137 / JCM 1170 / LMG 11437 / NCIMB 947 / NCTC 947)) Explore Q03R62 Go to UniProtKB: Q03R62
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q03R62
Sequence Annotations Expand
Reference Sequence

Small Molecules

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.46 Å
R-Value Free: 0.198 (Depositor), 0.203 (DCC)
R-Value Work: 0.163 (Depositor), 0.177 (DCC)
R-Value Observed: 0.164 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.867	α = 90
b = 50.962	β = 104.33
c = 49.289	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
SBC-Collect	data collection
HKL-3000	data reduction
HKL-3000	data scaling
SHELXD	phasing
MLPHARE	phasing
DM	phasing
SOLVE	phasing
RESOLVE	phasing
HKL-3000	phasing

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2009-07-14

Deposition Author(s):

Midwest Center for Structural Genomics (MCSG)

Revision History (Full details and data files)

Version 1.0: 2009-07-14
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Source and taxonomy, Version format compliance
Version 1.2: 2017-11-01
Changes: Refinement description
Version 1.3: 2024-11-20
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.