4BKN | pdb_00004bkn

Human Dihydropyrimidinase-related protein 3 (DPYSL3)

• PDB DOI: https://doi.org/10.2210/pdb4BKN/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2013-04-26 Released: 2013-05-08 
• Deposition Author(s): Mathea, S., Elkins, J.M., Alegre-Abarrategui, J., Shrestha, L., Burgess-Brown, N., Puranik, S., Coutandin, D., Bradley, A., Vollmar, M., von Delft, F., Bountra, C., Arrowsmith, C., Edwards, A., Knapp, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.238 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.197 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.199 (Depositor) 

Starting Model: experimental

Literature

Structure of Dpysl3

Mathea, S.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Macromolecule Content

• Total Structure Weight: 124.27 kDa 
• Atom Count: 7,760 
• Modelled Residue Count: 962 
• Deposited Residue Count: 1,142 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DIHYDROPYRIMIDINASE-RELATED PROTEIN 3	A, B	571	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for Q14195 (Homo sapiens) Explore Q14195  Go to UniProtKB:  Q14195
PHAROS:  Q14195 GTEx:  ENSG00000113657

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.238 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.197 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.199 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 144.23	α = 90
b = 96.65	β = 137.26
c = 119.27	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
Aimless	data scaling
CCP4	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-05-08 
Deposition Author(s): Mathea, S., Elkins, J.M., Alegre-Abarrategui, J., Shrestha, L., Burgess-Brown, N., Puranik, S., Coutandin, D., Bradley, A., Vollmar, M., von Delft, F., Bountra, C., Arrowsmith, C., Edwards, A., Knapp, S.

Revision History  

• Version 1.0: 2013-05-08
  Type: Initial release
  
• Version 1.1: 2023-12-20
  Changes: Data collection, Database references, Other, Refinement description