3VSN | pdb_00003vsn

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

• PDB DOI: https://doi.org/10.2210/pdb3VSN/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.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.194 (Depositor), 0.190 (DCC) 
• R-Value Work: 
  0.166 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.168 (Depositor) 

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.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 84.62 kDa 
• Atom Count: 5,786 
• Modeled Residue Count: 632 
• Deposited Residue Count: 659 
• Unique protein chains: 1

Macromolecules

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 EC: 4.2.2
UniProt
Find proteins for Q00704 (Autographa californica nuclear polyhedrosis virus) Explore Q00704  Go to UniProtKB:  Q00704

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
IOD	AB [auth A], AC [auth A], B [auth A], BB [auth A], BC [auth A], C [auth A], CB [auth A], CC [auth A], D [auth A], DB [auth A], DC [auth A], E [auth A], EB [auth A], EC [auth A], F [auth A], FA [auth A], FB [auth A], FC [auth A], G [auth A], GA [auth A], GB [auth A], H [auth A], HA [auth A], HB [auth A], I [auth A], IA [auth A], IB [auth A], J [auth A], JA [auth A], JB [auth A], K [auth A], KA [auth A], KB [auth A], L [auth A], LA [auth A], LB [auth A], M [auth A], MA [auth A], MB [auth A], N [auth A], NA [auth A], NB [auth A], O [auth A], OA [auth A], OB [auth A], P [auth A], PA [auth A], PB [auth A], Q [auth A], QA [auth A], QB [auth A], R [auth A], RA [auth A], RB [auth A], S [auth A], SA [auth A], SB [auth A], T [auth A], TA [auth A], TB [auth A], U [auth A], UA [auth A], UB [auth A], V [auth A], VA [auth A], VB [auth A], W [auth A], WA [auth A], WB [auth A], XA [auth A], XB [auth A], YA [auth A], YB [auth A], ZA [auth A], ZB [auth A]	IODIDE ION I XMBWDFGMSWQBCA-UHFFFAOYSA-M
GOL	AA [auth A], BA [auth A], CA [auth A], DA [auth A], EA [auth A], X [auth A], Y [auth A], Z [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.194 (Depositor), 0.190 (DCC) 
• R-Value Work:  0.166 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.168 (Depositor) 

Space Group: P 6₂

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 118.172	α = 90
b = 118.172	β = 90
c = 100.099	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-05-22 
Deposition Author(s): Kawaguchi, Y., Sugiura, N., Kimata, K., Kimura, M., Kakuta, Y.

Revision History  

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