5NGD | pdb_00005ngd

Crystal structure of the V325G mutant of the bacteriophage G20C portal protein

PDB DOI: https://doi.org/10.2210/pdb5NGD/pdb

Classification: TRANSPORT PROTEIN
Organism(s): Oshimavirus P7426
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2017-03-17 Released: 2017-03-29
Deposition Author(s): Pascoa, T., Jenkins, H.T., Chechik, M., Greive, S.J., Antson, A.A.
Funding Organization(s): Bilateral NSF/BIO-BBSRC, Wellcome Trust

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free:
0.225 (Depositor), 0.230 (DCC)
R-Value Work:
0.206 (Depositor), 0.210 (DCC)
R-Value Observed:
0.206 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

Porphyrin-Assisted Docking of a Thermophage Portal Protein into Lipid Bilayers: Nanopore Engineering and Characterization

Cressiot, B., Greive, S.J., Si, W., Pascoa, T.C., Mojtabavi, M., Chechik, M., Jenkins, H.T., Lu, X., Aksimentiev, A., Antson, A.A., Wanunu, M.

(2017) ACS Nano 11: 11931-11945

DOI: https://doi.org/10.1021/acsnano.7b06980

Macromolecule Content

Total Structure Weight: 183.93 kDa
Atom Count: 13,061
Modelled Residue Count: 1,607
Deposited Residue Count: 1,668
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Portal protein	A, B, C, D	417	Oshimavirus P7426	Mutation(s): 1 Gene Names: P74p85
UniProt
Find proteins for A7XXR3 (Thermus virus P74-26) Explore A7XXR3 Go to UniProtKB: A7XXR3
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A7XXR3
Sequence Annotations Expand
Reference Sequence LOADING

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.225 (Depositor), 0.230 (DCC)
R-Value Work: 0.206 (Depositor), 0.210 (DCC)
R-Value Observed: 0.206 (Depositor)

Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 223.234	α = 90
b = 223.234	β = 90
c = 115.817	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
DIALS	data reduction
Aimless	data scaling
SHELX	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2017-03-29

Deposition Author(s):

Funding Organization	Location	Grant Number
Bilateral NSF/BIO-BBSRC	United Kingdom	BB/N018729/1
Wellcome Trust	United Kingdom	101528/Z/13/Z

Revision History (Full details and data files)

Version 1.0: 2017-03-29
Type: Initial release
Version 1.1: 2018-08-01
Changes: Data collection, Database references
Version 1.2: 2024-05-08
Changes: Data collection, Database references, Refinement description

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.