5AXV

Crystal Structure of Cypovirus Polyhedra R13K Mutant

PDB DOI: https://doi.org/10.2210/pdb5AXV/pdb

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

Deposited: 2015-08-01 Released: 2015-11-11
Deposition Author(s): Abe, S., Ijiri, H., Negishi, H., Yamanaka, H., Sasaki, K., Hirata, K., Mori, H., Ueno, T.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.04 Å
R-Value Free:
0.206 (Depositor), 0.200 (DCC)
R-Value Work:
0.149 (Depositor), 0.150 (DCC)
R-Value Observed:
0.152 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Design of Enzyme-Encapsulated Protein Containers by In Vivo Crystal Engineering

Abe, S., Ijiri, H., Negishi, H., Yamanaka, H., Sasaki, K., Hirata, K., Mori, H., Ueno, T.

(2015) Adv Mater 27: 7951-7956

PubMed: 26503073 Search on PubMed
DOI: https://doi.org/10.1002/adma.201503827
Primary Citation of Related Structures:
5AXU, 5AXV

PubMed Abstract:
Crystalline protein assemblies of polyhedra crystal (PhC) can be utilized as solid enzyme containers for long-term storage of enzymes with retention of their enzymatic activity. The enzymes can be released from the crystals at the optimum pH for the enzymatic activity by dissolution of the crystals using in vivo crystal engineering.

Organizational Affiliation

Department of Biomolecular Engineering, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Nagatsuta-cho, 4259-B55, Midori-ku, Yokohama, 226-8501, Japan.

Macromolecule Content

Total Structure Weight: 29.06 kDa
Atom Count: 2,171
Modelled Residue Count: 248
Deposited Residue Count: 248
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Polyhedrin	A	248	Bombyx mori cypovirus 1	Mutation(s): 2
UniProt
Find proteins for P11041 (Bombyx mori cytoplasmic polyhedrosis virus) Explore P11041 Go to UniProtKB: P11041
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P11041
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CTP Query on CTP 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]	CYTIDINE-5'-TRIPHOSPHATE C₉ H₁₆ N₃ O₁₄ P₃ PCDQPRRSZKQHHS-XVFCMESISA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A]	D [auth A], E [auth A], F [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.04 Å
R-Value Free: 0.206 (Depositor), 0.200 (DCC)
R-Value Work: 0.149 (Depositor), 0.150 (DCC)
R-Value Observed: 0.152 (Depositor)

Space Group: I 2 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 103.381	α = 90
b = 103.381	β = 90
c = 103.381	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2015-11-11

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2015-11-11
Type: Initial release
Version 1.1: 2016-01-27
Changes: Database references
Version 1.2: 2020-02-26
Changes: Data collection, Derived calculations
Version 1.3: 2023-11-08
Changes: Data collection, Database references, Refinement description
Version 1.4: 2024-11-13
Changes: Structure summary