3D3Y | pdb_00003d3y

Crystal structure of a conserved protein from Enterococcus faecalis V583

• PDB DOI: https://doi.org/10.2210/pdb3D3Y/pdb

• Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
• Organism(s): Enterococcus faecalis V583
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-05-13 Released: 2008-07-15 
• Deposition Author(s): Tan, K., Li, H., Clancy, S., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 
  0.213 (Depositor), 0.212 (DCC) 
• R-Value Work: 
  0.172 (Depositor), 0.174 (DCC) 
• R-Value Observed: 
  0.174 (Depositor) 

Literature

The crystal structure of a conserved protein from Enterococcus faecalis V583.

Tan, K., Li, H., Clancy, S., Joachimiak, A.

To be published.

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 49.54 kDa 
• Atom Count: 3,682 
• Modeled Residue Count: 425 
• Deposited Residue Count: 425 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uncharacterized protein	A	425	Enterococcus faecalis V583	Mutation(s): 0  Gene Names: EF_3151
UniProt
Find proteins for Q82ZB5 (Enterococcus faecalis (strain ATCC 700802 / V583)) Explore Q82ZB5  Go to UniProtKB:  Q82ZB5

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	F [auth A], G [auth A], H [auth A], I [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
ACT	B [auth A], C [auth A], D [auth A], E [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

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: 1.95 Å
• R-Value Free:  0.213 (Depositor), 0.212 (DCC) 
• R-Value Work:  0.172 (Depositor), 0.174 (DCC) 
• R-Value Observed: 0.174 (Depositor) 

Space Group: I 4

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 122.437	α = 90
b = 122.437	β = 90
c = 69.003	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
SBC-Collect	data collection
HKL-3000	data reduction
HKL-3000	data scaling
SHELXD	phasing
MLPHARE	phasing
DM	phasing
RESOLVE	phasing
HKL-3000	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-07-15 
Deposition Author(s): Tan, K., Li, H., Clancy, S., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2008-07-15
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Source and taxonomy, Version format compliance
• Version 1.2: 2024-10-30
  Changes: Data collection, Database references, Derived calculations, Structure summary