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- PDB-4pds: Crystal structure of Rad53 kinase domain and SCD2 in complex with... -

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Basic information

Entry
Database: PDB / ID: 4pds
TitleCrystal structure of Rad53 kinase domain and SCD2 in complex with AMPPNP
ComponentsSerine/threonine-protein kinase RAD53
KeywordsTRANSFERASE / kinase domain / ANP / 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
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Serine/threonine-protein kinase RAD53
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsHo, C.S. / Wybenga-Groot, L.E. / Ceccarelli, D.F. / Sicheri, F.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)MOP36399 Canada
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 21, 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 1.4Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Sep 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 ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Serine/threonine-protein kinase RAD53
B: Serine/threonine-protein kinase RAD53
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,8664
Polymers76,8532
Non-polymers1,0122
Water00
1
A: Serine/threonine-protein kinase RAD53
hetero molecules

A: Serine/threonine-protein kinase RAD53
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,8664
Polymers76,8532
Non-polymers1,0122
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_454-x-1,y,-z-1/21
2
B: Serine/threonine-protein kinase RAD53
hetero molecules

B: Serine/threonine-protein kinase RAD53
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,8664
Polymers76,8532
Non-polymers1,0122
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Unit cell
Length a, b, c (Å)74.149, 77.539, 222.170
Angle α, β, γ (deg.)90.000, 90.000, 90.000
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 / Plasmid: pPROEx-Hta-TEV / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P22216, dual-specificity kinase
#2: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM

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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: 2.08 Å3/Da / Density % sol: 40.8 %
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: APS / Beamline: 14-ID-B / Wavelength: 0.9 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Nov 22, 2004
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.9→30 Å / Num. obs: 14414 / % possible obs: 98.7 % / Redundancy: 8.5 % / Biso Wilson estimate: 83.92 Å2 / Rmerge(I) obs: 0.097 / Net I/σ(I): 21.6
Reflection shellResolution: 2.9→3 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.648 / Mean I/σ(I) obs: 2.8 / % possible all: 97.8

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.8.4_1496)refinement
XDSdata scaling
CNSphasing
CNSrefinement
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4PDP

4pdp


Resolution: 2.9→29.213 Å / FOM work R set: 0.7912 / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 26.8 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.263 726 5.07 %
Rwork0.2273 13591 -
obs0.229 14317 97.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 227.28 Å2 / Biso mean: 90.69 Å2 / Biso min: 50.29 Å2
Refinement stepCycle: final / Resolution: 2.9→29.213 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3564 0 50 0 3614
Biso mean--105.69 --
Num. residues----497
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053681
X-RAY DIFFRACTIONf_angle_d0.8945013
X-RAY DIFFRACTIONf_chiral_restr0.036609
X-RAY DIFFRACTIONf_plane_restr0.008621
X-RAY DIFFRACTIONf_dihedral_angle_d13.3331213
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.9-3.1240.31961570.26242613277096
3.124-3.4380.25411440.226827082852100
3.438-3.93440.25981560.205127462902100
3.9344-4.95310.23581290.204427912920100
4.9531-29.21440.27281400.2482733287395
Refinement TLS params.Method: refined / Origin x: -12.9148 Å / Origin y: -4.7564 Å / Origin z: -27.8893 Å
111213212223313233
T0.574 Å20.1992 Å2-0.1263 Å2-0.5785 Å2-0.1844 Å2--0.4596 Å2
L1.9948 °2-1.5288 °20.618 °2-2.1492 °2-0.3443 °2--0.8566 °2
S-0.0523 Å °0.0344 Å °-0.0188 Å °-0.0575 Å °0.021 Å °0.0853 Å °-0.1198 Å °-0.0516 Å °0.0415 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA191 - 500
2X-RAY DIFFRACTION1allB191 - 500

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