3VSM

The crystal structure of novel chondroition lyase ODV-E66, baculovirus envelope protein

PDB DOI: https://doi.org/10.2210/pdb3VSM/pdb

Classification: LYASE ACTIVATOR
Organism(s): Autographa californica nucleopolyhedrovirus
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2012-04-27 Released: 2013-05-22
Deposition Author(s): Kawaguchi, Y., Sugiura, N., Kimata, K., Kimura, M., Kakuta, Y.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.206
R-Value Work: 0.172
R-Value Observed: 0.173

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

The crystal structure of novel chondroition lyase ODV-E66, baculovirus envelope protein

Kawaguchi, Y., Sugiura, N., Kimata, K., Kimura, M., Kakuta, Y.

To be published.

Macromolecule Content

Total Structure Weight: 74.46 kDa
Atom Count: 5,699
Modelled Residue Count: 633
Deposited Residue Count: 659
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Occlusion-derived virus envelope protein E66	A	659	Autographa californica nucleopolyhedrovirus	Mutation(s): 0 Gene Names: P79
UniProt
Find proteins for Q00704 (Autographa californica nuclear polyhedrosis virus) Explore Q00704 Go to UniProtKB: Q00704
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q00704
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A]	B [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.206
R-Value Work: 0.172
R-Value Observed: 0.173
Space Group: P 6₂

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 113.535	α = 90
b = 113.535	β = 90
c = 101.505	γ = 120

Software Package:

Software Name	Purpose
ADSC	data collection
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2013-05-22

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2013-05-22
Type: Initial release
Version 1.1: 2024-03-20
Changes: Data collection, Database references, Derived calculations

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.