5XSL | pdb_00005xsl

Crystal structure of the PWWP domain of human hepatoma-derived growth factor

• PDB DOI: https://doi.org/10.2210/pdb5XSL/pdb

• Classification: HORMONE
• Organism(s): Rattus norvegicus
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2017-06-14 Released: 2018-06-20 
• Deposition Author(s): Chen, L.Y., Huang, Y.C., Hsieh, Y.C., Lin, P.J., Chen, C.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.30 Å
• R-Value Free: 
  0.282 (Depositor), 0.290 (DCC) 
• R-Value Work: 
  0.225 (Depositor), 0.240 (DCC) 
• R-Value Observed: 
  0.229 (Depositor) 

Starting Model: experimental

Literature

Structure of the PWWP domain at 3.3 Angstroms resolution

Chen, L.Y., Huang, Y.C., Hsieh, Y.C., Lin, P.J.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 13.74 kDa 
• Atom Count: 702 
• Modeled Residue Count: 85 
• Deposited Residue Count: 120 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hepatoma-derived growth factor	A	120	Rattus norvegicus	Mutation(s): 0  Gene Names: Hdgf
UniProt
Find proteins for Q8VHK7 (Rattus norvegicus) Explore Q8VHK7  Go to UniProtKB:  Q8VHK7

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.30 Å
• R-Value Free:  0.282 (Depositor), 0.290 (DCC) 
• R-Value Work:  0.225 (Depositor), 0.240 (DCC) 
• R-Value Observed: 0.229 (Depositor) 

Space Group: P 6₄ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 79.49	α = 90
b = 79.49	β = 90
c = 105.099	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-06-20 
Deposition Author(s): Chen, L.Y., Huang, Y.C., Hsieh, Y.C., Lin, P.J., Chen, C.J.

Revision History  

• Version 1.0: 2018-06-20
  Type: Initial release
  
• Version 1.1: 2023-11-22
  Changes: Data collection, Database references, Refinement description
• Version 1.2: 2024-11-06
  Changes: Structure summary