1VPY | pdb_00001vpy

CRYSTAL STRUCTURE OF a DUF72 family protein (EF0366) FROM ENTEROCOCCUS FAECALIS V583 AT 2.52 A RESOLUTION

• PDB DOI: https://doi.org/10.2210/pdb1VPY/pdb

• Classification: UNKNOWN FUNCTION
• Organism(s): Enterococcus faecalis V583
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2004-11-23 Released: 2004-12-07 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.52 Å
• R-Value Free: 
  0.257 (Depositor), 0.261 (DCC) 
• R-Value Work: 
  0.225 (Depositor), 0.225 (DCC) 
• R-Value Observed: 
  0.227 (Depositor) 

Literature

Crystal structure of hypothetical protein (ef0366) from Enterococcus faecalis v583 at 2.52 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 34.36 kDa 
• Atom Count: 2,043 
• Modeled Residue Count: 251 
• Deposited Residue Count: 289 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEIN (hypothetical protein EF0366)	A	289	Enterococcus faecalis V583	Mutation(s): 9  Gene Names: ef0366
UniProt
Find proteins for Q838R9 (Enterococcus faecalis (strain ATCC 700802 / V583)) Explore Q838R9  Go to UniProtKB:  Q838R9

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	B [auth A], C [auth A], D [auth A], E [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
UNL	F [auth A]	Unknown ligand PTFCDOFLOPIGGS-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.52 Å
• R-Value Free:  0.257 (Depositor), 0.261 (DCC) 
• R-Value Work:  0.225 (Depositor), 0.225 (DCC) 
• R-Value Observed: 0.227 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M31VPY

Space Group: P 6₅

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 114.079	α = 90
b = 114.079	β = 90
c = 52.307	γ = 120

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
SHARP	phasing
REFMAC	refinement
CCP4	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-12-07 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2004-12-07
  Type: Initial release
  
• Version 1.1: 2008-04-26
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Advisory, Source and taxonomy, Version format compliance
• Version 1.3: 2017-10-11
  Changes: Data collection
• Version 1.4: 2023-01-25
  Changes: Database references, Derived calculations
• Version 1.5: 2024-10-16
  Changes: Data collection, Structure summary