3LVT

The Crystal Structure of a Protein in the Glycosyl Hydrolase Family 38 from Enterococcus faecalis to 2.55A

• PDB DOI: https://doi.org/10.2210/pdb3LVT/pdb

• Classification: HYDROLASE
• Organism(s): Enterococcus faecalis V583
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2010-02-22 Released: 2010-03-16 
• Deposition Author(s): Stein, A.J., Binkowski, T.A., Weger, A., Borovilos, M., Moy, S., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.55 Å
• R-Value Free: 
  0.282 (Depositor), 0.278 (DCC) 
• R-Value Work: 
  0.222 (Depositor), 0.218 (DCC) 
• R-Value Observed: 
  0.225 (Depositor) 

Literature

The Crystal Structure of a Protein in the Glycosyl Hydrolase Family 38 from Enterococcus faecalis to 2.55A

Stein, A.J., Binkowski, T.A., Weger, A., Borovilos, M., Moy, S., Joachimiak, A.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 103.55 kDa 
• Atom Count: 6,466 
• Modelled Residue Count: 833 
• Deposited Residue Count: 899 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycosyl hydrolase, family 38	A	899	Enterococcus faecalis V583	Mutation(s): 0  Gene Names: EF1707, EF_1707
UniProt
Find proteins for Q834E8 (Enterococcus faecalis (strain ATCC 700802 / V583)) Explore Q834E8  Go to UniProtKB:  Q834E8

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA	B [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-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: 2.55 Å
• R-Value Free:  0.282 (Depositor), 0.278 (DCC) 
• R-Value Work:  0.222 (Depositor), 0.218 (DCC) 
• R-Value Observed: 0.225 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 132.728	α = 90
b = 134.947	β = 90
c = 106.329	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
SBC-Collect	data collection
SHELX	phasing
MLPHARE	phasing
DM	phasing
RESOLVE	phasing
Coot	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-03-16 
Deposition Author(s): Stein, A.J., Binkowski, T.A., Weger, A., Borovilos, M., Moy, S., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2010-03-16
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-11-08
  Changes: Refinement description
• Version 1.3: 2024-11-27
  Changes: Data collection, Database references, Derived calculations, Structure summary