6IIP

Apo-form structure of the HRP3 PWWP domain

• PDB DOI: https://doi.org/10.2210/pdb6IIP/pdb

• Classification: DNA BINDING PROTEIN
• 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: 0.95 Å
• R-Value Free: 0.205 
• R-Value Work: 0.197 
• R-Value Observed: 0.197 

Starting Model: experimental

Literature

Apo-form structure of the HRP3 PWWP domain

Wang, Z., Tian, W.

(2019) Nucleic Acids Res 

Biological Assembly 1  

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

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

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

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

Macromolecule Content

• Total Structure Weight: 21.1 kDa 
• Atom Count: 1,775 
• Modelled Residue Count: 175 
• Deposited Residue Count: 176 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hepatoma-derived growth factor-related protein 3	A, B	88	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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MES	C [auth A], G [auth B]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C6 H13 N O4 S SXGZJKUKBWWHRA-UHFFFAOYSA-N
SO4	D [auth A], E [auth A], F [auth A], H [auth B], I [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 0.95 Å
• R-Value Free: 0.205 
• R-Value Work: 0.197 
• R-Value Observed: 0.197 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 38.478	α = 90
b = 39.931	β = 90
c = 97.385	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