6IIR

Complex structure of the HRP3 PWWP domain with a 10-bp GC-rich DNA

PDB DOI: https://doi.org/10.2210/pdb6IIR/pdb
NAKB: 6IIR

Classification: DNA BINDING PROTEIN/DNA
Organism(s): Homo sapiens, synthetic construct
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

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.258
R-Value Work: 0.202
R-Value Observed: 0.205

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Complex structure of the HRP3 PWWP domain with a 10-bp GC-rich DNA

Wang, Z., Tian, W.

(2019) Nucleic Acids Res

Macromolecule Content

Total Structure Weight: 29.25 kDa
Atom Count: 2,039
Modelled Residue Count: 217
Deposited Residue Count: 220
Unique protein chains: 1
Unique nucleic acid chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hepatoma-derived growth factor-related protein 3	A, B	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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9Y3E1
Protein Feature View Expand
Reference Sequence

Find similar nucleic acids by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Length	Organism	Image
10-bp GC-rich DNA	C, D	10	synthetic construct
Protein Feature View Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.258
R-Value Work: 0.202
R-Value Observed: 0.205
Space Group: P 3₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 33.554	α = 90
b = 33.554	β = 90
c = 197.913	γ = 120

Software Package:

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

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2019-04-24

Deposition Author(s):

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

Revision History (Full details and data files)

Version 1.0: 2019-04-24
Type: Initial release

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.