6IIQ | pdb_00006iiq

Complex structure of the HRP3 PWWP domain with a 16-bp TA-rich DNA

• PDB DOI: https://doi.org/10.2210/pdb6IIQ/pdb
• NAKB: 6IIQ

• Classification: DNA BINDING PROTEIN/DNA
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2018-10-07 Released: 2019-04-24 
• Deposition Author(s): Wang, Z., Tian, W.
• Funding Organization(s): National Natural Science Foundation of China

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 
  0.253 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.205 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.207 (Depositor) 

Starting Model: experimental

Literature

Complex structure of the HRP3 PWWP domain with a 16-bp TA-rich DNA

Wang, Z., Tian, W.

(2019) Nucleic Acids Res 

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: isothermal titration calorimetry

Macromolecule Content 

• Total Structure Weight: 54.99 kDa 
• Atom Count: 3,278 
• Modeled Residue Count: 325 
• Deposited Residue Count: 364 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hepatoma-derived growth factor-related protein 3	A, B, C	100	Homo sapiens	Mutation(s): 0  Gene Names: HDGFL3, HDGF2, HDGFRP3, CGI-142
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y3E1 (Homo sapiens) Explore Q9Y3E1  Go to UniProtKB:  Q9Y3E1
PHAROS:  Q9Y3E1 GTEx:  ENSG00000166503

Entity ID: 2
Molecule	Chains	Length	Organism	Image
16-bp TA-rich DNA	D, E, F, G	16	Homo sapiens

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TRS	I [auth A], K [auth B], M [auth C]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C4 H12 N O3 LENZDBCJOHFCAS-UHFFFAOYSA-O
MLA	H [auth A], J [auth B], L [auth C]	MALONIC ACID C3 H4 O4 OFOBLEOULBTSOW-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free:  0.253 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.205 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.207 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.426	α = 90
b = 33.556	β = 90.06
c = 201.151	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2019-04-24 
Deposition Author(s): Wang, Z., Tian, W.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China	China	31570729

Revision History  

• Version 1.0: 2019-04-24
  Type: Initial release
  
• Version 1.1: 2023-11-22
  Changes: Data collection, Database references, Refinement description