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)

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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) 

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.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

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

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

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
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

Entry History 

Deposition Data

• Released Date: 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)

Revision History  

• 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