1YV9 | pdb_00001yv9

Crystal structure of a HAD-like phosphatase from Enterococcus faecalis V583

• PDB DOI: https://doi.org/10.2210/pdb1YV9/pdb

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


• Deposited: 2005-02-15 Released: 2005-03-15 
• Deposition Author(s): Seetharaman, J., Swaminathan, S., Burley, S.K., New York SGX Research Center for Structural Genomics (NYSGXRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 
  0.280 (Depositor), 0.280 (DCC) 
• R-Value Work: 
  0.219 (Depositor), 0.220 (DCC) 
• R-Value Observed: 
  0.219 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of a Hypothetical protein, hydrolase haloacid dehalogenase-like family

Seetharaman, J., Swaminathan, S.

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.

Macromolecule Content 

• Total Structure Weight: 58.52 kDa 
• Atom Count: 4,156 
• Modeled Residue Count: 514 
• Deposited Residue Count: 528 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
hydrolase, haloacid dehalogenase family	A, B	264	Enterococcus faecalis V583	Mutation(s): 0  EC: 3.1.3
UniProt
Find proteins for Q836C7 (Enterococcus faecalis (strain ATCC 700802 / V583)) Explore Q836C7  Go to UniProtKB:  Q836C7

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4	C [auth A], D [auth A], E [auth B], F [auth B]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free:  0.280 (Depositor), 0.280 (DCC) 
• R-Value Work:  0.219 (Depositor), 0.220 (DCC) 
• R-Value Observed: 0.219 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 117.628	α = 90
b = 126.114	β = 90
c = 112.634	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-03-15 
Deposition Author(s): Seetharaman, J., Swaminathan, S., Burley, S.K., New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History  

• Version 1.0: 2005-03-15
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Source and taxonomy, Version format compliance
• Version 1.3: 2021-02-03
  Changes: Database references, Derived calculations, Structure summary
• Version 1.4: 2023-08-23
  Changes: Data collection, Database references, Refinement description