6LEE | pdb_00006lee

Crystal structure of Cypovirus Polyhedra mutant with deletion of Ala67-Ala104

PDB DOI: https://doi.org/10.2210/pdb6LEE/pdb

Classification: VIRAL PROTEIN
Organism(s): Bombyx mori cypovirus 1
Expression System: Spodoptera frugiperda
Mutation(s): Yes

Deposited: 2019-11-25 Released: 2020-12-09
Deposition Author(s): Abe, S., Kasamatsu, M., Hirata, K., Yamashita, K., Ueno, T.
Funding Organization(s): Japan Society for the Promotion of Science

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free:
0.250 (Depositor), 0.224 (DCC)
R-Value Work:
0.187 (Depositor)
R-Value Observed:
0.193 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 6LEE

This is version 1.4 of the entry. See complete history.

Literature

In-Cell Engineering of Protein Crystals with Nanoporous Structures for Promoting Cascade Reactions

Nguyen, T.K., Abe, S., Kasamatsu, M., Maity, B., Yamashita, K., Hirata, K., Kojima, M., Ueno, T.

(2021) ACS Appl Nano Mater 4: 1672-1681

DOI: https://doi.org/10.1021/acsanm.0c03129

Macromolecule Content

Total Structure Weight: 23.93 kDa
Atom Count: 1,661
Modeled Residue Count: 199
Deposited Residue Count: 210
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Polyhedrin	A	210	Bombyx mori cypovirus 1	Mutation(s): 1
UniProt
Find proteins for P11041 (Bombyx mori cytoplasmic polyhedrosis virus) Explore P11041 Go to UniProtKB: P11041
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P11041
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free: 0.250 (Depositor), 0.224 (DCC)
R-Value Work: 0.187 (Depositor)
R-Value Observed: 0.193 (Depositor)

Space Group: I 2 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 103.84	α = 90
b = 103.84	β = 90
c = 103.84	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XSCALE	data scaling
PHENIX	phasing
XDS	data processing

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2020-12-09

Deposition Author(s):

Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science	Japan	JP17H05872

Revision History (Full details and data files)

Version 1.0: 2020-12-09
Type: Initial release
Version 1.1: 2021-04-07
Changes: Database references
Version 1.2: 2021-04-14
Changes: Database references
Version 1.3: 2023-11-22
Changes: Data collection, Database references, Refinement description
Version 1.4: 2024-10-16
Changes: Structure summary

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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.