4ZJN | pdb_00004zjn

Crystal structure of the bacteriophage G20C portal protein

PDB DOI: https://doi.org/10.2210/pdb4ZJN/pdb

Classification: TRANSPORT PROTEIN
Organism(s): Bacteriophage sp.
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2015-04-29 Released: 2015-05-27
Deposition Author(s): Williams, L.S., Turkenburg, J.P., Levdikov, V.M., Minakhin, L., Severinov, K., Antson, A.A.
Funding Organization(s): Wellcome Trust

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.98 Å
R-Value Free:
0.205 (Depositor), 0.205 (DCC)
R-Value Work:
0.175 (Depositor), 0.175 (DCC)
R-Value Observed:
0.175 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 4ZJN

This is version 1.1 of the entry. See complete history.

Literature

Crystal structure of the bacteriophage G20C portal protein

Williams, L.S., Turkenburg, J.P., Levdikov, V.M., Minakhin, L., Severinov, K., Antson, A.A.

To be published.

Macromolecule Content

Total Structure Weight: 142 kDa
Atom Count: 10,134
Modeled Residue Count: 1,233
Deposited Residue Count: 1,278
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Portal protein	A, B, C	426	Bacteriophage sp.	Mutation(s): 0
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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MPD Query on MPD Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth B] SDF format, chain F [auth C] MOL2 format, chain D [auth A] MOL2 format, chain E [auth B] MOL2 format, chain F [auth C] mmCIF format, chain D [auth A] mmCIF format, chain E [auth B] mmCIF format, chain F [auth C]	D [auth A], E [auth B], F [auth C]	(4S)-2-METHYL-2,4-PENTANEDIOL C₆ H₁₄ O₂ SVTBMSDMJJWYQN-YFKPBYRVSA-N		Interactions Focus chain D [auth A] Focus chain E [auth B] Focus chain F [auth C] Interactions & Density Focus chain D [auth A] Focus chain E [auth B] Focus chain F [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.98 Å
R-Value Free: 0.205 (Depositor), 0.205 (DCC)
R-Value Work: 0.175 (Depositor), 0.175 (DCC)
R-Value Observed: 0.175 (Depositor)

Space Group: P 4 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 155.328	α = 90
b = 155.328	β = 90
c = 115.445	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2015-05-27

Deposition Author(s):

Turkenburg, J.P.

Funding Organization	Location	Grant Number
Wellcome Trust	United Kingdom	098230

Revision History (Full details and data files)

Version 1.0: 2015-05-27
Type: Initial release
Version 1.1: 2024-05-08
Changes: Data collection, Database references

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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.