5XSK | pdb_00005xsk

Crystal structure of PWWP-DNA complex for human hepatoma-derived growth factor

• PDB DOI: https://doi.org/10.2210/pdb5XSK/pdb
• NAKB: 5XSK

• Classification: HORMONE
• Organism(s): Escherichia coli BL21, 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: 2.84 Å
• R-Value Free: 
  0.269 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.191 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.195 (Depositor) 

Starting Model: experimental

Literature

Structure of PWWP-DNA complex at 2.84 Angstroms resolution

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

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 33.8 kDa 
• Atom Count: 1,903 
• Modeled Residue Count: 201 
• Deposited Residue Count: 260 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Hepatoma-derived growth factor	C [auth A], D [auth B]	120	Rattus norvegicus	Mutation(s): 0  Gene Names: Hdgf
UniProt
Find proteins for Q8VHK7 (Rattus norvegicus) Explore Q8VHK7  Go to UniProtKB:  Q8VHK7

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(P*TP*TP*CP*AP*AP*GP*AP*CP*CP*A)-3')	A [auth D]	10	Escherichia coli BL21

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(P*TP*GP*GP*TP*CP*TP*TP*GP*AP*A)-3')	B [auth F]	10	Escherichia coli BL21

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MPD (Subject of Investigation/LOI)	E [auth A], F [auth B]	(4S)-2-METHYL-2,4-PENTANEDIOL C6 H14 O2 SVTBMSDMJJWYQN-YFKPBYRVSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.84 Å
• R-Value Free:  0.269 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.191 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.195 (Depositor) 

Space Group: P 3₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 32.402	α = 90
b = 32.402	β = 90
c = 205.82	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: 2018-06-27
  Changes: Data collection, Derived calculations
• Version 1.2: 2023-11-22
  Changes: Data collection, Database references, Refinement description