6YNG | pdb_00006yng

MicroED structure of granulin determined from five native nanocrystalline granulovirus occlusion bodies

PDB DOI: https://doi.org/10.2210/pdb6YNG/pdb

Classification: VIRAL PROTEIN
Organism(s): Cydia pomonella granulosis virus (isolate Mexican)
Mutation(s): No

Deposited: 2020-04-13 Released: 2020-04-29
Deposition Author(s): Bunker, R.D.

Experimental Data Snapshot

Method: ELECTRON CRYSTALLOGRAPHY
Resolution: 2.80 Å
R-Value Free:
0.226 (Depositor), 0.271 (DCC)
R-Value Work:
0.184 (Depositor), 0.216 (DCC)
R-Value Observed:
0.188 (Depositor)

Starting Model: experimental
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This is version 1.2 of the entry. See complete history.

Literature

MicroED structure of granulin determined from five native nanocrystalline granulovirus occlusion bodies

Bunker, R.D.

To be published.

Macromolecule Content

Total Structure Weight: 29.38 kDa
Atom Count: 2,048
Modeled Residue Count: 243
Deposited Residue Count: 248
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Granulin	A	248	Cydia pomonella granulosis virus (isolate Mexican)	Mutation(s): 0
UniProt
Find proteins for P87577 (Cydia pomonella granulosis virus (isolate Mexico/1963)) Explore P87577 Go to UniProtKB: P87577
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P87577
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: ELECTRON CRYSTALLOGRAPHY
Resolution: 2.80 Å
R-Value Free: 0.226 (Depositor), 0.271 (DCC)
R-Value Work: 0.184 (Depositor), 0.216 (DCC)
R-Value Observed: 0.188 (Depositor)

Space Group: I 2 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 103.657	α = 90
b = 103.657	β = 90
c = 103.657	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX

Structure Validation

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Entry History

Deposition Data

Released Date: 2020-04-29

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2020-04-29
Type: Initial release
Version 1.1: 2023-08-09
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.2: 2024-02-14
Changes: Data collection, Refinement description

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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.