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), 0.229 (DCC)
R-Value Work:
0.206 (Depositor), 0.213 (DCC)
R-Value Observed:
0.206 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 5NGD

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
Modeled Residue Count: 1,607
Deposited Residue Count: 1,668
Unique protein chains: 1

Macromolecules

Find similar proteins by:

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 phage P74-26) Explore A7XXR3 Go to UniProtKB: A7XXR3
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A7XXR3
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.225 (Depositor), 0.229 (DCC)
R-Value Work: 0.206 (Depositor), 0.213 (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

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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

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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.