4QF0 | pdb_00004qf0

Structure of a 16 nm protein cage designed by fusing symmetric oligomeric domains, quadruple mutant, P21212 form

PDB DOI: https://doi.org/10.2210/pdb4QF0/pdb

Classification: OXIDOREDUCTASE, VIRAL PROTEIN
Organism(s): Kitasatospora aureofaciens, Influenza A virus
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2014-05-19 Released: 2015-05-20
Deposition Author(s): Lai, Y.-T., Yeates, T.O.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 6.49 Å
R-Value Free:
0.324 (Depositor), 0.331 (DCC)
R-Value Work:
0.271 (Depositor), 0.273 (DCC)
R-Value Observed:
0.274 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 4QF0

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

Literature

Structural transition of a protein nanocage as a function of pH and salt concentration.

Lai, Y.-T., Yeates, T.O.

To be published.

Macromolecule Content

Total Structure Weight: 301.14 kDa
Atom Count: 20,256
Modeled Residue Count: 2,646
Deposited Residue Count: 2,736
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Non-haem bromoperoxidase BPO-A2, Matrix protein 1 chimera	A, B, C, D, E A, B, C, D, E, F	456	Kitasatospora aureofaciens, Influenza A virus This entity is chimeric	Mutation(s): 3 Gene Names: bpoA2, M EC: 1.11.1
UniProt
Find proteins for P03485 (Influenza A virus (strain A/Puerto Rico/8/1934 H1N1)) Explore P03485 Go to UniProtKB: P03485
Find proteins for P29715 (Kitasatospora aureofaciens) Explore P29715 Go to UniProtKB: P29715
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Groups	P29715 P03485
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 6.49 Å
R-Value Free: 0.324 (Depositor), 0.331 (DCC)
R-Value Work: 0.271 (Depositor), 0.273 (DCC)
R-Value Observed: 0.274 (Depositor)

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 175.5	α = 90
b = 147.73	β = 90
c = 167.63	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

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Entry History

Deposition Data

Released Date: 2015-05-20

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2015-05-20
Type: Initial release
Version 1.1: 2017-07-26
Changes: Refinement description, Source and taxonomy
Version 1.2: 2024-02-28
Changes: Data collection, Database references, 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.