4XVN | pdb_00004xvn

Crystal structure of the small terminase from thermophilic phage G20C

PDB DOI: https://doi.org/10.2210/pdb4XVN/pdb

Classification: VIRAL PROTEIN
Organism(s): Thermus phage G20c
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2015-01-27 Released: 2016-02-10
Deposition Author(s): Loredo-Varela, J., Jenkins, H.T., Chechik, M., Greive, S.J., Antson, A.A.
Funding Organization(s): Wellcome Trust, Consejo Nacional de Ciencia y Tecnologia de Mexico

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free:
0.276 (Depositor), 0.290 (DCC)
R-Value Work:
0.249 (Depositor), 0.260 (DCC)
R-Value Observed:
0.250 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of the small terminase from thermophilic phage G20C

Antson, A.A., Loredo-Varela, J., Jenkins, H.T., Chechik, M., Greive, S.J.

To be published.

Macromolecule Content

Total Structure Weight: 116.27 kDa
Atom Count: 6,209
Modeled Residue Count: 795
Deposited Residue Count: 1,044
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Small terminase	A, B, C, D, E A, B, C, D, E, F	174	Thermus phage G20c	Mutation(s): 0
UniProt
Find proteins for A0A1L4BKP6 (Thermus phage G20c) Explore A0A1L4BKP6 Go to UniProtKB: A0A1L4BKP6
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A1L4BKP6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B, C, D, E A, B, C, D, E, F	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free: 0.276 (Depositor), 0.290 (DCC)
R-Value Work: 0.249 (Depositor), 0.260 (DCC)
R-Value Observed: 0.250 (Depositor)

Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 152.585	α = 90
b = 152.585	β = 90
c = 108.805	γ = 120

Software Package:

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

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2016-02-10

Deposition Author(s):

Loredo-Varela, J.

Funding Organization	Location	Grant Number
Wellcome Trust	United Kingdom	098230
Consejo Nacional de Ciencia y Tecnologia de Mexico	Mexico	--

Revision History (Full details and data files)

Version 1.0: 2016-02-10
Type: Initial release
Version 1.1: 2024-10-16
Changes: Data collection, Database references, Structure summary

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.