2QR4 | pdb_00002qr4

Crystal structure of oligoendopeptidase-F from Enterococcus faecium

PDB DOI: https://doi.org/10.2210/pdb2QR4/pdb

Classification: HYDROLASE
Organism(s): Enterococcus faecium DO
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2007-07-27 Released: 2007-08-14
Deposition Author(s): Ramagopal, U.A., Toro, R., Meyer, A.J., Freeman, J., Bain, K., Rodgers, L., Sauder, J.M., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free:
0.244 (Depositor), 0.241 (DCC)
R-Value Work:
0.188 (Depositor), 0.186 (DCC)
R-Value Observed:
0.191 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 2QR4

This is version 1.5 of the entry. See complete history.

Literature

Crystal structure of oligoendopeptidase-F from Enterococcus faecium.

Ramagopal, U.A., Toro, R., Meyer, A.J., Freeman, J., Bain, K., Rodgers, L., Sauder, J.M., Burley, S.K., Almo, S.C.

To be published.

Macromolecule Content

Total Structure Weight: 137 kDa
Atom Count: 8,549
Modeled Residue Count: 1,027
Deposited Residue Count: 1,174
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptidase M3B, oligoendopeptidase F	A, B	587	Enterococcus faecium DO	Mutation(s): 0 Gene Names: EfaeDRAFT_1000 EC: 3.4.24
UniProt
Find proteins for I3U4V7 (Enterococcus faecium (strain ATCC BAA-472 / TX0016 / DO)) Explore I3U4V7 Go to UniProtKB: I3U4V7
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	I3U4V7
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: 2.50 Å
R-Value Free: 0.244 (Depositor), 0.241 (DCC)
R-Value Work: 0.188 (Depositor), 0.186 (DCC)
R-Value Observed: 0.191 (Depositor)

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 133.142	α = 90
b = 133.142	β = 90
c = 171.619	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
CBASS	data collection
HKL-2000	data reduction
SHELXD	phasing
SHELXE	model building

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2007-08-14

Deposition Author(s):

Ramagopal, U.A.

New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History (Full details and data files)

Version 1.0: 2007-08-14
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Refinement description, Source and taxonomy, Version format compliance
Version 1.2: 2017-10-25
Changes: Refinement description
Version 1.3: 2018-11-14
Changes: Data collection, Structure summary
Version 1.4: 2021-02-03
Changes: Database references, Derived calculations, Structure summary
Version 1.5: 2024-10-30
Changes: Data collection, Database references, Refinement description, 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.