3OQ0 | pdb_00003oq0

Crystal Structure of motif N of Saccharomyces cerevisiae Dbf4

• PDB DOI: https://doi.org/10.2210/pdb3OQ0/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: 2.70 Å
• R-Value Free: 
  0.244 (Depositor) 
• R-Value Work: 
  0.205 (Depositor), 0.205 (DCC) 
• R-Value Observed: 
  0.207 (Depositor) 

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 and generated by PISA (software)

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

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

Biological assembly 3 assigned by authors and generated by PISA (software)

Biological Assembly 4  

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

Biological assembly 4 assigned by authors and generated by PISA (software)

Biological Assembly 5  

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

Biological assembly 5 assigned by authors and generated by PISA (software)

Biological Assembly 6  

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

Biological assembly 6 assigned by authors and generated by PISA (software)

Biological Assembly 7  

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

Biological assembly 7 assigned by authors and generated by PISA (software)

Biological Assembly 8  

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

Biological assembly 8 assigned by authors and generated by PISA (software)

Biological Assembly 9  

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

Biological assembly 9 assigned by authors and generated by PISA (software)

Biological Assembly 10  

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

Biological assembly 10 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 177.46 kDa 
• Atom Count: 8,369 
• Modeled Residue Count: 984 
• Deposited Residue Count: 1,510 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DBF4	A, B, C, D, E, F, G, H, I, J	151	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

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B, C, D, E, F, G, H, I, J	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free:  0.244 (Depositor) 
• R-Value Work:  0.205 (Depositor), 0.205 (DCC) 
• R-Value Observed: 0.207 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 90.221	α = 90
b = 79.358	β = 110.74
c = 127.419	γ = 90

Software Package:

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

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: 2024-11-06
  Changes: Data collection, Database references, Derived calculations, Structure summary