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- PDB-3oq4: Crystal Structure of motif N of Saccharomyces cerevisiae Dbf4 -

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Basic information

Entry
Database: PDB / ID: 3oq4
TitleCrystal Structure of motif N of Saccharomyces cerevisiae Dbf4
ComponentsDBF4
KeywordsCELL CYCLE / DDK / BRCT / Rad53 / replication checkpoint / FHA domain / regulatory subunit of DDK / cdc7 / phosphorylation / nuclear
Function / homology
Function and homology information


positive regulation of kinetochore assembly / positive regulation of meiotic DNA double-strand break formation / positive regulation of DNA replication initiation / negative regulation of exit from mitosis / Dbf4-dependent protein kinase complex / positive regulation of meiosis I / positive regulation of nuclear cell cycle DNA replication / regulation of cell cycle phase transition / premeiotic DNA replication / Activation of the pre-replicative complex ...positive regulation of kinetochore assembly / positive regulation of meiotic DNA double-strand break formation / positive regulation of DNA replication initiation / negative regulation of exit from mitosis / Dbf4-dependent protein kinase complex / positive regulation of meiosis I / positive regulation of nuclear cell cycle DNA replication / regulation of cell cycle phase transition / premeiotic DNA replication / Activation of the pre-replicative complex / Activation of ATR in response to replication stress / mitotic DNA replication checkpoint signaling / DNA replication origin binding / chromosome, centromeric region / DNA replication initiation / protein serine/threonine kinase activator activity / chromosome segregation / cell division / centrosome / chromatin / zinc ion binding / nucleus / cytoplasm
Similarity search - Function
Regulatory subunit Dfp1/Him1, central region / : / Dfp1/Him1, central region / BRCT domain / Zinc finger, DBF-type / DBF-type zinc finger superfamily / : / DBF zinc finger / Zinc finger DBF4-type profile. / Zinc finger in DBF-like proteins ...Regulatory subunit Dfp1/Him1, central region / : / Dfp1/Him1, central region / BRCT domain / Zinc finger, DBF-type / DBF-type zinc finger superfamily / : / DBF zinc finger / Zinc finger DBF4-type profile. / Zinc finger in DBF-like proteins / BRCT domain / BRCT domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
DDK kinase regulatory subunit DBF4
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsMatthews, L.A. / Jones, D.R. / Prasad, A.A. / Duncker, B.P. / Guarne, A.
Citation
Journal: To be Published
Title: Crystal Structure of Saccharomyces cerevisiae Dbf4-motif N
Authors: Matthews, L.A. / Jones, D.R. / Prasad, A.A. / Duncker, B.P. / Guarne, A.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2009
Title: Crystallization and preliminary X-ray diffraction analysis of motif N from Saccharomyces cerevisiae Dbf4
Authors: Matthews, L.A. / Duong, A. / Prasad, A.A. / Duncker, B.P. / Guarne, A.
History
DepositionSep 2, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 7, 2011Provider: repository / Type: Initial release
Revision 1.1Sep 6, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DBF4
B: DBF4
C: DBF4
D: DBF4
E: DBF4


Theoretical massNumber of molelcules
Total (without water)78,1145
Polymers78,1145
Non-polymers00
Water4,143230
1
A: DBF4


Theoretical massNumber of molelcules
Total (without water)15,6231
Polymers15,6231
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: DBF4


Theoretical massNumber of molelcules
Total (without water)15,6231
Polymers15,6231
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: DBF4


Theoretical massNumber of molelcules
Total (without water)15,6231
Polymers15,6231
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: DBF4


Theoretical massNumber of molelcules
Total (without water)15,6231
Polymers15,6231
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: DBF4


Theoretical massNumber of molelcules
Total (without water)15,6231
Polymers15,6231
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)83.714, 99.707, 127.045
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein
DBF4 / Protein DNA52


Mass: 15622.896 Da / Num. of mol.: 5 / Fragment: residues 120-250
Source method: isolated from a genetically manipulated source
Details: Dbf4 residues 120-250 cloned in the multicloning site of pET15b using NdeI-BamHI
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: D4205, DBF4, DNA52, YD9609.07C, YDR052C / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)STARpRarepLysS / References: UniProt: P32325
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 230 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.39 Å3/Da / Density % sol: 63.76 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.1
Details: 22% MPD (v/v) and 100 mM Na/K phosphate buffer pH 7.1, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.0809 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 10, 2009 / Details: mirrors
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0809 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. all: 42401 / Num. obs: 42318 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.2 % / Rmerge(I) obs: 0.192 / Rsym value: 0.206 / Net I/σ(I): 8.92
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsRsym valueDiffraction-ID% possible all
2.4-2.445.90.7372.60.5021100
6.51-505.90.1529.860.194199.1
5.17-6.5160.1599.960.199199.9
4.52-5.1760.14910.840.174199.8
4.1-4.526.10.15310.220.181199.8
3.81-4.16.20.1739.170.294199.9
3.58-3.816.30.1685.260.197199.9
3.41-3.586.30.1799.230.2561100
3.26-3.416.30.17510.10.1761100
3.13-3.266.30.2039.850.2021100
3.02-3.136.30.2178.70.1971100
2.93-3.026.30.2518.740.219199.9
2.85-2.936.30.2897.90.25199.9
2.77-2.856.30.3267.020.277199.9
2.7-2.776.30.3646.140.286199.9
2.64-2.76.30.5024.790.809199.9
2.59-2.646.30.5434.260.418199.9
2.53-2.596.30.6043.80.455199.8
2.49-2.536.20.6063.670.537199.8
2.44-2.496.10.6233.330.436199.5

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Processing

Software
NameVersionClassification
CBASSdata collection
PHASERphasing
PHENIX(phenix.refine: 1.4_159)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3OQ0

3oq0


Resolution: 2.4→46.408 Å / SU ML: 0.27 / σ(F): 1.34 / Phase error: 24.85 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2288 2146 5.08 %
Rwork0.2036 --
obs0.2049 42245 99.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.376 Å2 / ksol: 0.336 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-17.8963 Å2-0 Å2-0 Å2
2---1.5453 Å2-0 Å2
3----16.351 Å2
Refinement stepCycle: LAST / Resolution: 2.4→46.408 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4327 0 0 230 4557
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074429
X-RAY DIFFRACTIONf_angle_d0.9465953
X-RAY DIFFRACTIONf_dihedral_angle_d13.9731714
X-RAY DIFFRACTIONf_chiral_restr0.065683
X-RAY DIFFRACTIONf_plane_restr0.003739
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3991-2.48480.32721980.24623954X-RAY DIFFRACTION99
2.4848-2.58430.27782200.24783908X-RAY DIFFRACTION100
2.5843-2.70190.31651910.25254015X-RAY DIFFRACTION100
2.7019-2.84430.2742320.23123947X-RAY DIFFRACTION100
2.8443-3.02250.2322160.22473958X-RAY DIFFRACTION100
3.0225-3.25580.25252050.20874006X-RAY DIFFRACTION100
3.2558-3.58340.22982130.20233997X-RAY DIFFRACTION100
3.5834-4.10160.19142030.18394031X-RAY DIFFRACTION100
4.1016-5.16650.19312050.16874091X-RAY DIFFRACTION100
5.1665-46.4170.21572630.20324192X-RAY DIFFRACTION99

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