2XPJ | pdb_00002xpj

Crystal structure of Physalis Mottle Virus with intact ordered RNA

PDB DOI: https://doi.org/10.2210/pdb2XPJ/pdb
NAKB: 2XPJ

Classification: VIRUS
Organism(s): Physalis mottle virus
Mutation(s): No

Deposited: 2010-08-26 Released: 2010-09-15
Deposition Author(s): Sagurthi, S.R., Rajaram, V., Savithri, H.S., Murthy, M.R.N.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.40 Å
R-Value Free:
0.311 (Depositor), 0.586 (DCC)
R-Value Work:
0.308 (Depositor), 0.583 (DCC)
R-Value Observed:
0.308 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.2 of the entry. See complete history.

Literature

Crystal Structure of Natural Bottom Component of Phmv

Sagurthi, S.R., Rajaram, V., Savithri, H.S., Murthy, M.R.N.

To be published.

Macromolecule Content

Total Structure Weight: 60.84 kDa
Atom Count: 4,001
Modeled Residue Count: 533
Deposited Residue Count: 567
Unique protein chains: 1
Unique nucleic acid chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
COAT PROTEIN	A, B, C	188	Physalis mottle virus	Mutation(s): 0
UniProt
Find proteins for P36351 (Physalis mottle virus) Explore P36351 Go to UniProtKB: P36351
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P36351
Sequence Annotations Expand
Reference Sequence

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Molecule	Chains	Length	Organism	Image
Entity ID: 2
5'-R(CPCPCP)-3'	D	3	N/A
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.40 Å
R-Value Free: 0.311 (Depositor), 0.586 (DCC)
R-Value Work: 0.308 (Depositor), 0.583 (DCC)
R-Value Observed: 0.308 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 285.4	α = 62.92
b = 288.36	β = 65.3
c = 290.61	γ = 60.85

Software Package:

Software Name	Purpose
CNS	refinement
AUTOMAR	data reduction
SCALEPACK	data scaling
AMoRE	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2010-09-15

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2010-09-15
Type: Initial release
Version 1.1: 2012-02-08
Changes: Other, Version format compliance
Version 1.2: 2023-12-20
Changes: Data collection, Database references, Derived calculations, Other, 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.