2R2Z | pdb_00002r2z

The crystal structure of a hemolysin domain from Enterococcus faecalis V583

• PDB DOI: https://doi.org/10.2210/pdb2R2Z/pdb

• Classification: TOXIN
• Organism(s): Enterococcus faecalis V583
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2007-08-28 Released: 2007-09-04 
• Deposition Author(s): Zhang, R., Tan, K., Zhou, M., Bargassa, M., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.20 Å
• R-Value Free: 
  0.171 (Depositor), 0.172 (DCC) 
• R-Value Work: 
  0.154 (Depositor), 0.156 (DCC) 
• R-Value Observed: 
  0.155 (Depositor) 

Literature

The crystal structure of a hemolysin domain from Enterococcus faecalis V583.

Zhang, R., Tan, K., Zhou, M., Bargassa, M., Joachimiak, A.

To be published.

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 11.03 kDa 
• Atom Count: 890 
• Modeled Residue Count: 84 
• Deposited Residue Count: 93 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemolysin	A	93	Enterococcus faecalis V583	Mutation(s): 0  Gene Names: EF_0700
UniProt
Find proteins for Q837X5 (Enterococcus faecalis (strain ATCC 700802 / V583)) Explore Q837X5  Go to UniProtKB:  Q837X5

Small Molecules

Ligands 1 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

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: 1.20 Å
• R-Value Free:  0.171 (Depositor), 0.172 (DCC) 
• R-Value Work:  0.154 (Depositor), 0.156 (DCC) 
• R-Value Observed: 0.155 (Depositor) 

Space Group: P 6₅

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 39.494	α = 90
b = 39.494	β = 90
c = 101.258	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-09-04 
Deposition Author(s): Zhang, R., Tan, K., Zhou, M., Bargassa, M., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2007-09-04
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Source and taxonomy, Version format compliance
• Version 1.2: 2024-10-30
  Changes: Data collection, Database references, Derived calculations, Structure summary