4P55

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)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.248 
• R-Value Work: 0.210 
• R-Value Observed: 0.212 

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.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by (software)

Macromolecule Content

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

Macromolecules

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

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
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 
• R-Value Work: 0.210 
• R-Value Observed: 0.212 
• 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

Entry History & Funding Information

Deposition Data

• Released Date: 2015-04-15 
Deposition Author(s): Hu, H.D., Gao, Z.Q., Lan, K., Dong, Y.H.

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

Revision History  

• 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