4P55 | pdb_00004p55

Crystal structure of DNA binding domain of K11 from KSHV

PDB DOI: https://doi.org/10.2210/pdb4P55/pdb

Classification: DNA BINDING PROTEIN
Organism(s): Human herpesvirus 8 strain GK18
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2014-03-14 Released: 2015-04-15
Deposition Author(s): Hu, H.D., Gao, Z.Q., Lan, K., Dong, Y.H.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free:
0.248 (Depositor), 0.245 (DCC)
R-Value Work:
0.210 (Depositor), 0.212 (DCC)
R-Value Observed:
0.212 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 4P55

This is version 1.3 of the entry. See complete history.

Literature

crystal structure of DNA binding domain of K11 from KSHV

Hu, H.D., Gao, Z.Q., Lan, K., Dong, Y.H.

To be published.

Macromolecule Content

Total Structure Weight: 26.19 kDa
Atom Count: 1,784
Modeled Residue Count: 201
Deposited Residue Count: 216
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Viral IRF2-like protein	A, B	108	Human herpesvirus 8 strain GK18	Mutation(s): 0 Gene Names: vIRF-2
UniProt
Find proteins for Q2HR71 (Human herpesvirus 8 type P (isolate GK18)) Explore Q2HR71 Go to UniProtKB: Q2HR71
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q2HR71
Sequence Annotations Expand
Reference Sequence

Small Molecules

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.248 (Depositor), 0.245 (DCC)
R-Value Work: 0.210 (Depositor), 0.212 (DCC)
R-Value Observed: 0.212 (Depositor)

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.467	α = 90
b = 48.467	β = 90
c = 195.088	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2015-04-15

Deposition Author(s):

Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	10979005 and 31200552

Revision History (Full details and data files)

Version 1.0: 2015-04-15
Type: Initial release
Version 1.1: 2020-01-08
Changes: Advisory, Author supporting evidence, Database references, Derived calculations, Other, Source and taxonomy
Version 1.2: 2023-12-27
Changes: Data collection, Database references, Refinement description
Version 1.3: 2024-11-20
Changes: Structure summary

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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.