3LVT | pdb_00003lvt

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)

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)

wwPDB Validation 3D Report Full Report

Validation slider image for 3LVT

This is version 1.3 of the entry. See complete history.

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.

Macromolecule Content

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

Macromolecules

Find similar proteins by:

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q834E8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on 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

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2010-03-16

Deposition Author(s):

Binkowski, T.A.

Midwest Center for Structural Genomics (MCSG)

Revision History (Full details and data files)

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

RCSB PDB is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

CoreTrustSeal

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.