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- PDB-6ya6: Minimal construct of Cdc7-Dbf4 bound to XL413 -

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Basic information

Entry
Database: PDB / ID: 6ya6
TitleMinimal construct of Cdc7-Dbf4 bound to XL413
Components
  • Cell division cycle 7-related protein kinase,Cell division cycle 7-related protein kinase,Cell division cycle 7-related protein kinase
  • Protein DBF4 homolog A
KeywordsCELL CYCLE / kinase / cdc7 / dbf4 / bivalent substrate / transferase
Function / homology
Function and homology information


Dbf4-dependent protein kinase complex / regulation of cell cycle phase transition / positive regulation of nuclear cell cycle DNA replication / mitotic DNA damage checkpoint signaling / cell cycle phase transition / double-strand break repair via break-induced replication / intercellular bridge / Transcriptional Regulation by E2F6 / Activation of the pre-replicative complex / enzyme activator activity ...Dbf4-dependent protein kinase complex / regulation of cell cycle phase transition / positive regulation of nuclear cell cycle DNA replication / mitotic DNA damage checkpoint signaling / cell cycle phase transition / double-strand break repair via break-induced replication / intercellular bridge / Transcriptional Regulation by E2F6 / Activation of the pre-replicative complex / enzyme activator activity / Activation of ATR in response to replication stress / positive regulation of G2/M transition of mitotic cell cycle / protein serine/threonine kinase activator activity / G1/S transition of mitotic cell cycle / mitotic spindle / kinase activity / DNA replication / nucleic acid binding / nuclear body / non-specific serine/threonine protein kinase / protein kinase activity / phosphorylation / cell division / protein serine kinase activity / protein serine/threonine kinase activity / positive regulation of cell population proliferation / signal transduction / zinc ion binding / nucleoplasm / ATP binding / metal ion binding / nucleus / cytoplasm
Similarity search - Function
Zinc finger, DBF-type / DBF-type zinc finger superfamily / DBF zinc finger / Zinc finger DBF4-type profile. / Zinc finger in DBF-like proteins / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site ...Zinc finger, DBF-type / DBF-type zinc finger superfamily / DBF zinc finger / Zinc finger DBF4-type profile. / Zinc finger in DBF-like proteins / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Chem-0SX / BORIC ACID / IMIDAZOLE / DI(HYDROXYETHYL)ETHER / Cell division cycle 7-related protein kinase / Protein DBF4 homolog A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.44 Å
AuthorsDick, S.D. / Cherepanov, P.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
The Francis Crick InstituteFC10061 United Kingdom
CitationJournal: Structure / Year: 2020
Title: Structural Basis for the Activation and Target Site Specificity of CDC7 Kinase.
Authors: Dick, S.D. / Federico, S. / Hughes, S.M. / Pye, V.E. / O'Reilly, N. / Cherepanov, P.
History
DepositionMar 11, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 27, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 1, 2020Group: Database references / Category: citation
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Aug 19, 2020Group: Database references / Derived calculations / Category: citation / struct_conn / struct_conn_type
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id
Revision 1.3Jan 24, 2024Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cell division cycle 7-related protein kinase,Cell division cycle 7-related protein kinase,Cell division cycle 7-related protein kinase
B: Protein DBF4 homolog A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,9279
Polymers57,2342
Non-polymers6937
Water8,359464
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7530 Å2
ΔGint-47 kcal/mol
Surface area21730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.640, 61.640, 233.910
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein Cell division cycle 7-related protein kinase,Cell division cycle 7-related protein kinase,Cell division cycle 7-related protein kinase / huCdc7


Mass: 40230.449 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CDC7, CDC7L1 / Production host: Escherichia coli (E. coli)
References: UniProt: O00311, non-specific serine/threonine protein kinase
#2: Protein Protein DBF4 homolog A / Activator of S phase kinase / Chiffon homolog A / DBF4-type zinc finger-containing protein 1


Mass: 17003.393 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DBF4, ASK, DBF4A, ZDBF1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9UBU7

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Non-polymers , 7 types, 471 molecules

#3: Chemical ChemComp-0SX / 8-chloro-2-[(2S)-pyrrolidin-2-yl][1]benzofuro[3,2-d]pyrimidin-4(3H)-one


Mass: 289.717 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H12ClN3O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical ChemComp-BO3 / BORIC ACID / Boric acid


Mass: 61.833 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: BH3O3
#7: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#8: Chemical ChemComp-IMD / IMIDAZOLE / Imidazole


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 464 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.15 Å3/Da / Density % sol: 42.72 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 0.1M PCTP pH7, 18% PEG 1500, 8% MPD

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 1.0332 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 21, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.44→59.61 Å / Num. obs: 82613 / % possible obs: 100 % / Redundancy: 9.1 % / Biso Wilson estimate: 13.58 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.049 / Net I/σ(I): 26.4
Reflection shellResolution: 1.44→1.491 Å / Rmerge(I) obs: 0.584 / Num. unique obs: 7764 / CC1/2: 0.77

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Processing

Software
NameVersionClassification
PHENIXdev_3707refinement
PHENIXdev_3707refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5MH9

5mh9
PDB Unreleased entry


Resolution: 1.44→42.85 Å / SU ML: 0.1286 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 17.0071
RfactorNum. reflection% reflection
Rfree0.1933 4139 5.02 %
Rwork0.1666 --
obs0.1679 82484 99.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 20.95 Å2
Refinement stepCycle: LAST / Resolution: 1.44→42.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3551 0 39 464 4054
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00583684
X-RAY DIFFRACTIONf_angle_d0.8884980
X-RAY DIFFRACTIONf_chiral_restr0.0799550
X-RAY DIFFRACTIONf_plane_restr0.0054636
X-RAY DIFFRACTIONf_dihedral_angle_d18.2031388
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.44-1.460.24931450.23942416X-RAY DIFFRACTION94.19
1.46-1.470.27091250.22612478X-RAY DIFFRACTION95.84
1.47-1.490.22461250.21192474X-RAY DIFFRACTION97.27
1.49-1.510.22981300.20812590X-RAY DIFFRACTION98.84
1.51-1.530.24641300.19882592X-RAY DIFFRACTION100
1.53-1.550.19611270.19332594X-RAY DIFFRACTION100
1.55-1.570.21271120.18282590X-RAY DIFFRACTION100
1.57-1.60.19541330.18762572X-RAY DIFFRACTION100
1.6-1.620.22571290.17372646X-RAY DIFFRACTION100
1.62-1.650.17461230.17672554X-RAY DIFFRACTION100
1.65-1.680.18361440.16962601X-RAY DIFFRACTION100
1.68-1.710.21321340.16632592X-RAY DIFFRACTION99.96
1.71-1.740.21141470.16332572X-RAY DIFFRACTION100
1.74-1.780.1811320.17092588X-RAY DIFFRACTION100
1.78-1.810.17461520.16952613X-RAY DIFFRACTION99.96
1.81-1.860.18741190.17322618X-RAY DIFFRACTION100
1.86-1.90.20571310.17462584X-RAY DIFFRACTION100
1.9-1.950.21361560.16652589X-RAY DIFFRACTION100
1.95-2.010.1881630.16212570X-RAY DIFFRACTION99.96
2.01-2.080.21421490.16342618X-RAY DIFFRACTION100
2.08-2.150.16991460.16542605X-RAY DIFFRACTION100
2.15-2.240.19581390.15992630X-RAY DIFFRACTION100
2.24-2.340.18311290.16392651X-RAY DIFFRACTION100
2.34-2.460.2031420.16272655X-RAY DIFFRACTION100
2.46-2.620.18871220.16422654X-RAY DIFFRACTION100
2.62-2.820.18741640.16922658X-RAY DIFFRACTION100
2.82-3.10.19491580.16832657X-RAY DIFFRACTION99.96
3.1-3.550.17921540.15772683X-RAY DIFFRACTION100
3.55-4.470.17751330.14332766X-RAY DIFFRACTION99.93
4.47-42.850.18821460.1642935X-RAY DIFFRACTION99.58
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)
10.0970182230177-0.05597423436410.05512722539580.1435410845060.0573132997861.00112283186-0.0106043402131-0.0217857696531-0.02810481395640.0204722080829-0.00781838239698-0.0218530050925-0.002866918268210.0657230060911-0.006919188300450.0771277502718-0.0003235502269620.004757817026620.106642312580.01226153010430.095170768653920.931083025814.90320099358.743664391
20.427327239976-0.2980575356070.02176398727670.0965422641431-0.09383538000930.05244646780730.03498031009170.021178230583-0.08971279567920.0145935599868-0.02650953071410.05440353574850.0171158512911-0.0144484437705-0.006626658449530.07613436463990.004384583629220.01061979131290.120429240246-0.002399462123040.1036300998551.4401974630517.760190793138.0656831905
30.2461814118050.01245563445840.08813555541220.291122626774-0.02623688790950.3156116375260.003786097498210.194348692868-0.0309991616088-0.05964713469470.0298428986234-0.06986930858020.01566824808390.06422585756840.01750183158530.06397146755310.007360138070940.01991857151840.1514248206610.00345870849050.096348010961421.306673506316.591556183130.6833103358
40.343582284356-0.082968659057-0.0865345538797-0.1889717398060.1409731153140.09512740465740.01843075981970.0937228985068-0.06284570965180.0716753175492-0.0337525036133-0.00376222287074-0.00274758942511-0.0329523554384-0.01576765590950.0959142192088-0.01230102679770.0127154595880.1181280795680.03203805962470.162588883541-2.8525177727126.412400218235.4799257847
50.04022396458950.03962872737860.03870826377430.06917290834270.07057274581920.314173854498-0.1639134284210.1093404031320.06393058141730.05523176904140.1208830698530.323192458551-0.479062236288-0.362849659798-0.008465831865120.2228252817230.1014198972570.04042761823410.4296637837610.1355138572240.277188617858-1.6126121871420.560375386268.4009669403
60.1296532103790.0303292692032-0.0377578208721-0.0113237498217-0.02689919847990.176637057787-0.0139241911883-0.19307601841-0.1278250602390.1269633642060.05724201060310.0162496659816-0.00111981149842-0.06029671612260.005534709721380.1427215008620.01063427674590.04501119950940.15526717640.03667152460220.15165839183116.29515070410.151276692276.2319149377
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 38:214)
2X-RAY DIFFRACTION2(chain A and resid 215:450 or chain D and resid 1:1)
3X-RAY DIFFRACTION3(chain A and resid 451:573)
4X-RAY DIFFRACTION4(chain B and resid 207:254)
5X-RAY DIFFRACTION5(chain B and resid 293:314 or chain D and resid 2:2)
6X-RAY DIFFRACTION6(chain B and resid 315:346)

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