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- PDB-3qbz: Crystal structure of the Rad53-recognition domain of Saccharomyce... -

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Basic information

Entry
Database: PDB / ID: 3qbz
TitleCrystal structure of the Rad53-recognition domain of Saccharomyces cerevisiae Dbf4
ComponentsDDK kinase regulatory subunit DBF4
KeywordsCELL CYCLE / FHA domain / Rad53 / replication checkpoint
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 / BRCT domain superfamily
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: 2.692 Å
AuthorsMatthews, L.A. / Jones, D.R. / Prasad, A.A. / Duncker, B.P. / Guarne, A.
Citation
Journal: J.Biol.Chem. / Year: 2012
Title: Saccharomyces cerevisiae Dbf4 has unique fold necessary for interaction with Rad53 kinase.
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
DepositionJan 14, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 7, 2011Provider: repository / Type: Initial release
Revision 1.1Dec 21, 2011Group: Database references
Revision 1.2Feb 20, 2013Group: Database references
Revision 1.3Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DDK kinase regulatory subunit DBF4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,2824
Polymers18,9941
Non-polymers2883
Water18010
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: DDK kinase regulatory subunit DBF4
hetero molecules

A: DDK kinase regulatory subunit DBF4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,5648
Polymers37,9882
Non-polymers5766
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_555-y,-x,-z+1/31
Buried area2890 Å2
ΔGint-82 kcal/mol
Surface area15880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.740, 83.740, 103.669
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number181
Space group name H-MP6422

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Components

#1: Protein DDK kinase regulatory subunit DBF4 / Dumbbell forming protein 4


Mass: 18993.949 Da / Num. of mol.: 1 / Fragment: residues 66-221, HBRCT domain
Source method: isolated from a genetically manipulated source
Details: Dbf4 residues 66-221 subcloned in 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 STAR pRAREpLysS / References: UniProt: P32325
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 10 / 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: 2.76 Å3/Da / Density % sol: 55.47 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 1.9 M ammonium sulfate 50 mM sodium cacodylate 15 mM CYMAL-7, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 10, 2010 / Details: mirrors
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.69→50 Å / Num. obs: 6371 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.9 % / Biso Wilson estimate: 53.46 Å2 / Rmerge(I) obs: 0.057 / Rsym value: 0.042 / Net I/σ(I): 31
Reflection shellResolution: 2.69→2.74 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.419 / Mean I/σ(I) obs: 3.5 / Num. unique all: 298 / Rsym value: 0.344 / % possible all: 99.7

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Processing

Software
NameVersionClassification
CBASSdata collection
PHASERphasing
PHENIX(phenix.refine: 1.6.4_486)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3OQ4

3oq4


Resolution: 2.692→38.823 Å / SU ML: 0.43 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.2729 300 4.72 %random
Rwork0.2238 ---
all0.2264 6373 --
obs0.2264 6361 99.81 %-
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 42.732 Å2 / ksol: 0.315 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-7.7673 Å2-0 Å2-0 Å2
2--7.7673 Å2-0 Å2
3----15.5345 Å2
Refinement stepCycle: LAST / Resolution: 2.692→38.823 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1038 0 15 10 1063
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081074
X-RAY DIFFRACTIONf_angle_d1.0341449
X-RAY DIFFRACTIONf_dihedral_angle_d16.07412
X-RAY DIFFRACTIONf_chiral_restr0.068161
X-RAY DIFFRACTIONf_plane_restr0.004178
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs
2.6923-3.39180.34181520.257529283080
3.3918-38.82720.24721480.212131333281
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.93080.1381-0.36840.8821-1.50073.574-0.01680.11320.1651-1.36660.39530.44250.85960.0376-0.16960.4678-0.1353-0.05250.2152-0.09250.392-21.336418.906719.213
21.8316-0.2710.05790.12190.22221.11290.0993-0.086-0.28140.222-0.18-0.08020.30330.11320.06430.4928-0.1595-0.07760.20110.03670.2101-27.5838-5.649120.8475
35.8636-1.7303-5.05274.6724.11376.38-1.68640.25670.90421.54860.9564-1.00961.4584-0.51290.58220.83950.1592-0.15420.3363-0.12770.369-34.6185-15.9327-3.8087
44.4966-1.85550.66183.23031.21855.932-0.24150.3853-0.57560.4407-0.2533-0.14220.31011.09320.39920.51810.11760.07720.40150.04690.3961-25.7734-13.73091.174
51.94040.1215-0.61362.3719-1.07050.42890.03050.4071-0.366-0.07150.0479-0.50660.93710.2136-0.12390.5833-0.1332-0.13230.41160.01660.1656-25.1499-13.429716.878
61.90.0280.77680.1240.13461.2021-0.18940.19-0.21680.03210.3388-0.1422-0.19970.6653-0.01620.4459-0.1241-0.0330.09730.05590.1997-36.203-11.927914.7589
72.4371.6546-0.70317.3273-3.66461.93281.0081-0.11810.1902-1.2217-0.74970.9922-0.31650.682-0.27810.5304-0.08390.08310.20790.00560.2724-47.7855-12.426810.4345
82.2127-0.34010.15840.2054-0.46230.8870.03280.0008-0.03680.621-0.16720.257-0.10840.2994-0.08670.5649-0.16230.02290.0651-0.02370.2407-43.2594-11.950918.9753
92.57590.0534-1.0321.7480.09941.246-0.237-0.03210.4755-0.16970.16370.5563-0.0683-0.08430.06230.4608-0.1452-0.03270.25110.03010.3119-29.8266-2.597811.9125
103.2786-3.378-2.68184.60071.20196.66240.73440.61230.4261-1.02350.6263-0.58580.48780.778-1.3690.6811-0.1972-0.12890.5084-0.16820.2314-17.9068-1.334811.5798
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A and resid 98:109
2X-RAY DIFFRACTION2chain A and resid 110:132
3X-RAY DIFFRACTION3chain A and resid 133:138
4X-RAY DIFFRACTION4chain A and resid 139:149
5X-RAY DIFFRACTION5chain A and resid 150:166
6X-RAY DIFFRACTION6chain A and resid 167:179
7X-RAY DIFFRACTION7chain A and resid 180:189
8X-RAY DIFFRACTION8chain A and resid 190:199
9X-RAY DIFFRACTION9chain A and resid 200:213
10X-RAY DIFFRACTION10chain A and resid 214:219

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