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- PDB-4pdp: Crystal structure of Rad53 kinase domain and SCD2 -

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Basic information

Entry
Database: PDB / ID: 4pdp
TitleCrystal structure of Rad53 kinase domain and SCD2
ComponentsSerine/threonine-protein kinase RAD53
KeywordsTRANSFERASE / Ser/Thr kinase domain / N-lobe / C-lobe / activation segment exchange
Function / homology
Function and homology information


deoxyribonucleoside triphosphate biosynthetic process / meiotic recombination checkpoint signaling / negative regulation of phosphorylation / dual-specificity kinase / calcium/calmodulin-dependent protein kinase activity / DNA replication origin binding / negative regulation of DNA damage checkpoint / DNA replication initiation / regulation of DNA repair / protein serine/threonine/tyrosine kinase activity ...deoxyribonucleoside triphosphate biosynthetic process / meiotic recombination checkpoint signaling / negative regulation of phosphorylation / dual-specificity kinase / calcium/calmodulin-dependent protein kinase activity / DNA replication origin binding / negative regulation of DNA damage checkpoint / DNA replication initiation / regulation of DNA repair / protein serine/threonine/tyrosine kinase activity / DNA damage checkpoint signaling / protein localization / cellular response to oxidative stress / protein tyrosine kinase activity / calmodulin binding / protein kinase activity / phosphorylation / DNA repair / protein serine kinase activity / protein serine/threonine kinase activity / ATP binding / nucleus / cytoplasm / cytosol
Similarity search - Function
Serine/threonine-protein kinase Rad53 / Forkhead associated domain / Forkhead-associated (FHA) domain profile. / FHA domain / Forkhead-associated (FHA) domain / SMAD/FHA domain superfamily / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 ...Serine/threonine-protein kinase Rad53 / Forkhead associated domain / Forkhead-associated (FHA) domain profile. / FHA domain / Forkhead-associated (FHA) domain / SMAD/FHA domain superfamily / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / 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 / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Serine/threonine-protein kinase RAD53
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.591 Å
AuthorsWybenga-Groot, L.E. / Ho, C.S. / Ceccarelli, D.F. / Sicheri, F.
CitationJournal: Cell Signal. / Year: 2014
Title: Structural basis of Rad53 kinase activation by dimerization and activation segment exchange.
Authors: Wybenga-Groot, L.E. / Ho, C.S. / Sweeney, F.D. / Ceccarelli, D.F. / McGlade, C.J. / Durocher, D. / Sicheri, F.
History
DepositionApr 19, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 28, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 1, 2014Group: Database references
Revision 1.2Nov 22, 2017Group: Derived calculations / Other ...Derived calculations / Other / Refinement description / Source and taxonomy
Category: entity_src_gen / pdbx_database_status ...entity_src_gen / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list / software
Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible ..._entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_oper_list.symmetry_operation / _software.classification
Revision 1.3Jul 17, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.name / _software.version
Revision 1.4Sep 27, 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 / refine_hist
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: Serine/threonine-protein kinase RAD53
B: Serine/threonine-protein kinase RAD53


Theoretical massNumber of molelcules
Total (without water)76,8532
Polymers76,8532
Non-polymers00
Water00
1
A: Serine/threonine-protein kinase RAD53

A: Serine/threonine-protein kinase RAD53


Theoretical massNumber of molelcules
Total (without water)76,8532
Polymers76,8532
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
2
B: Serine/threonine-protein kinase RAD53

B: Serine/threonine-protein kinase RAD53


Theoretical massNumber of molelcules
Total (without water)76,8532
Polymers76,8532
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Unit cell
Length a, b, c (Å)76.430, 79.070, 227.710
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Serine/threonine-protein kinase RAD53 / CHEK2 homolog / Serine-protein kinase 1


Mass: 38426.664 Da / Num. of mol.: 2 / Fragment: Kinase domain and SCD2 (UNP residues 170-512) / Mutation: A225S,D339A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: RAD53, MEC2, SAD1, SPK1, YPL153C, P2588 / Production host: Escherichia coli (E. coli) / References: UniProt: P22216, dual-specificity kinase

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.24 Å3/Da / Density % sol: 45.05 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 30% v/v PEG400, 50 mM sodium citrate, 100 mM Tris, pH 8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.99 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 20, 2004
RadiationMonochromator: Rosenbaum-Rock double crystal sagittal focusing
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99 Å / Relative weight: 1
ReflectionResolution: 2.591→56.89 Å / Num. obs: 21728 / % possible obs: 94.5 % / Redundancy: 6.1 % / Rmerge(I) obs: 0.067 / Net I/σ(I): 15.3
Reflection shellResolution: 2.591→2.7 Å / Redundancy: 3 % / Rmerge(I) obs: 0.153 / Mean I/σ(I) obs: 2.4 / % possible all: 70.2

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.8.4_1496)refinement
XDSdata reduction
CNSphasing
CNSrefinement
REFMACrefinement
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1IG1

1ig1


Resolution: 2.591→29.855 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 27.46 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2611 1521 6.98 %Random
Rwork0.2273 ---
obs0.2296 21720 98.97 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.591→29.855 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3880 0 0 0 3880
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033944
X-RAY DIFFRACTIONf_angle_d0.6135347
X-RAY DIFFRACTIONf_dihedral_angle_d10.9661356
X-RAY DIFFRACTIONf_chiral_restr0.024635
X-RAY DIFFRACTIONf_plane_restr0.005679
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.591-2.63570.34611260.33991654X-RAY DIFFRACTION84
2.6357-2.68360.31841420.29881871X-RAY DIFFRACTION100
2.6836-2.73510.31441510.29461969X-RAY DIFFRACTION100
2.7351-2.79090.30881400.28481899X-RAY DIFFRACTION100
2.7909-2.85160.28791480.27841905X-RAY DIFFRACTION100
2.8516-2.91780.32361430.29431963X-RAY DIFFRACTION100
2.9178-2.99070.28221430.29251890X-RAY DIFFRACTION100
2.9907-3.07150.28911470.26061960X-RAY DIFFRACTION100
3.0715-3.16180.30461450.23481903X-RAY DIFFRACTION100
3.1618-3.26380.26641430.24471944X-RAY DIFFRACTION100
3.2638-3.38030.25691420.22781905X-RAY DIFFRACTION100
3.3803-3.51540.25611480.23151922X-RAY DIFFRACTION100
3.5154-3.67510.22581450.23411977X-RAY DIFFRACTION100
3.6751-3.86850.28881440.22261891X-RAY DIFFRACTION100
3.8685-4.11030.25111420.20511911X-RAY DIFFRACTION100
4.1103-4.42670.23931480.19451926X-RAY DIFFRACTION100
4.4267-4.87050.25011350.18781947X-RAY DIFFRACTION100
4.8705-5.57130.24261420.21011931X-RAY DIFFRACTION100
5.5713-7.00420.27391470.24971925X-RAY DIFFRACTION100
7.0042-29.85690.24461400.21721848X-RAY DIFFRACTION96
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)
12.70441.64210.96042.86620.20271.1274-0.75660.1983-0.2216-0.33111.12870.7354-0.11020.10260.15831.017-1.1966-0.63660.8010.48731.090317.05026.331917.3316
22.7272-1.0518-0.98110.36170.25014.63680.3935-0.01250.89330.415-1.14660.2519-1.88791.24610.22951.0701-0.4084-0.43670.70520.1911.00640.90961.697319.6223
31.95242.3657-0.23293.12630.44844.3175-0.27050.18740.4698-0.11740.04020.1278-0.54250.12020.20750.6669-0.3272-0.26280.80540.35430.7031.6206-9.319915.7481
44.4784-0.2933-1.38013.8001-1.17713.1146-0.16570.3372-0.2266-0.95060.32430.12871.0438-0.5801-0.00630.8522-0.4437-0.23920.8030.27670.674-4.0122-23.917112.3504
53.5877-0.83430.20723.6823-1.56187.57850.7106-0.99160.60040.0679-0.5152-0.57440.5180.24250.97071.1153-0.699-0.52541.22430.3680.86344.9219-19.546240.8333
61.03110.3795-1.07732.27971.56513.086-0.1354-0.5016-0.67650.23950.36130.0854-0.26551.06770.02011.0525-0.4316-0.34631.3120.46871.11014.6421-33.504141.3247
74.59192.75731.43033.2548-0.38494.58080.2188-0.44870.0410.3177-0.3931-0.6724-0.03670.36380.08840.7763-0.4398-0.28320.75670.27580.7206-9.4568-34.288539.458
82.9197-1.29570.69914.9645-1.21772.52480.1173-1.0935-0.49730.8996-0.02580.09110.8683-1.025-0.1731.1579-0.5678-0.31761.16960.35030.7961-20.1568-47.731649.3844
92.44020.82351.71732.93550.18243.1641-0.49250.23240.4839-0.73860.31021.0616-0.3124-0.80860.09061.0761-0.4182-0.310.97580.31140.9616-28.8265-34.091735.6512
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 191 through 229 )
2X-RAY DIFFRACTION2chain 'A' and (resid 230 through 258 )
3X-RAY DIFFRACTION3chain 'A' and (resid 259 through 385 )
4X-RAY DIFFRACTION4chain 'A' and (resid 386 through 494 )
5X-RAY DIFFRACTION5chain 'B' and (resid 191 through 222 )
6X-RAY DIFFRACTION6chain 'B' and (resid 223 through 249 )
7X-RAY DIFFRACTION7chain 'B' and (resid 250 through 358 )
8X-RAY DIFFRACTION8chain 'B' and (resid 359 through 456 )
9X-RAY DIFFRACTION9chain 'B' and (resid 457 through 496 )

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