3OQ4 | pdb_00003oq4

Crystal Structure of motif N of Saccharomyces cerevisiae Dbf4

• PDB DOI: https://doi.org/10.2210/pdb3OQ4/pdb

• Classification: CELL CYCLE
• Organism(s): Saccharomyces cerevisiae
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2010-09-02 Released: 2011-09-07 
• Deposition Author(s): Matthews, L.A., Jones, D.R., Prasad, A.A., Duncker, B.P., Guarne, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 
  0.229 (Depositor), 0.232 (DCC) 
• R-Value Work: 
  0.204 (Depositor), 0.202 (DCC) 
• R-Value Observed: 
  0.205 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of Saccharomyces cerevisiae Dbf4-motif N

Matthews, L.A., Jones, D.R., Prasad, A.A., Duncker, B.P., Guarne, A.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Biological Assembly 3  

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

Biological assembly 3 assigned by authors.

Biological Assembly 4  

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

Biological assembly 4 assigned by authors.

Biological Assembly 5  

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

Biological assembly 5 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 78.11 kDa 
• Atom Count: 4,592 
• Modeled Residue Count: 520 
• Deposited Residue Count: 670 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DBF4	A, B, C, D, E	134	Saccharomyces cerevisiae	Mutation(s): 0  Gene Names: D4205, DBF4, DNA52, YD9609.07C, YDR052C
UniProt
Find proteins for P32325 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P32325  Go to UniProtKB:  P32325

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free:  0.229 (Depositor), 0.232 (DCC) 
• R-Value Work:  0.204 (Depositor), 0.202 (DCC) 
• R-Value Observed: 0.205 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 83.714	α = 90
b = 99.707	β = 90
c = 127.045	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-09-07 
Deposition Author(s): Matthews, L.A., Jones, D.R., Prasad, A.A., Duncker, B.P., Guarne, A.

Revision History  

• Version 1.0: 2011-09-07
  Type: Initial release
  
• Version 1.1: 2023-09-06
  Changes: Data collection, Database references, Refinement description