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- PDB-5xzv: Crystal structure of Rad53 1-466 in complex with AMP-PNP -

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Basic information

Entry
Database: PDB / ID: 5xzv
TitleCrystal structure of Rad53 1-466 in complex with AMP-PNP
ComponentsSerine/threonine-protein kinase RAD53
KeywordsTRANSFERASE / serine/threonine-protein kinase / FHA domain / checkpoint kinase
Function / homology
Function and homology information


deoxyribonucleoside triphosphate biosynthetic process / G2/M DNA damage checkpoint / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / meiotic recombination checkpoint signaling / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / negative regulation of phosphorylation / dual-specificity kinase / DNA replication origin binding / negative regulation of DNA damage checkpoint ...deoxyribonucleoside triphosphate biosynthetic process / G2/M DNA damage checkpoint / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / meiotic recombination checkpoint signaling / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / negative regulation of phosphorylation / dual-specificity kinase / 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 / protein tyrosine kinase activity / protein kinase activity / phosphorylation / DNA repair / protein serine kinase activity / protein serine/threonine kinase activity / ATP binding / nucleus / cytosol / cytoplasm
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 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain ...Serine/threonine-protein kinase Rad53 / Forkhead associated domain / Forkhead-associated (FHA) domain profile. / FHA domain / Forkhead-associated (FHA) domain / SMAD/FHA domain superfamily / 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
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: 3.1 Å
AuthorsWeng, J.H. / Tsai, M.D.
CitationJournal: Biochemistry / Year: 2017
Title: Phospho-Priming Confers Functionally Relevant Specificities for Rad53 Kinase Autophosphorylation
Authors: Chen, E.S. / Weng, J.H. / Chen, Y.H. / Wang, S.C. / Liu, X.X. / Huang, W.C. / Matsui, T. / Kawano, Y. / Liao, J.H. / Lim, L.H. / Bessho, Y. / Huang, K.F. / Wu, W.J. / Tsai, M.D.
History
DepositionJul 14, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 11, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_radiation_wavelength.wavelength

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,0254
Polymers105,0132
Non-polymers1,0122
Water0
1
A: Serine/threonine-protein kinase RAD53
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,0132
Polymers52,5061
Non-polymers5061
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area19670 Å2
MethodPISA
2
B: Serine/threonine-protein kinase RAD53
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,0132
Polymers52,5061
Non-polymers5061
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area560 Å2
ΔGint2 kcal/mol
Surface area17880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.690, 116.690, 140.804
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

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


Mass: 52506.469 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 1-466
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: RAD53, MEC2, SAD1, SPK1, YPL153C, P2588 / Production host: Escherichia coli (E. coli) / 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: 2.66 Å3/Da / Density % sol: 53.68 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 100MM CACODYLATE BUFFER, 0.4M NACL, 1.5M (NH4)2SO4 / PH range: 6.5

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11101
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONNSRRC BL15A111
SYNCHROTRONSPring-8 BL41XU21
Detector
TypeIDDetectorDate
RAYONIX MX300HE1CCDJul 20, 2016
DECTRIS PILATUS3 6M2PIXELJun 24, 2016
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
111
21
ReflectionResolution: 3.1→30 Å / Num. obs: 20517 / % possible obs: 99.6 % / Redundancy: 11 % / Biso Wilson estimate: 46.3 Å2 / Rmerge(I) obs: 0.064 / Net I/σ(I): 16.3
Reflection shellResolution: 3.1→3.21 Å / Redundancy: 11.1 % / Rmerge(I) obs: 0.848 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.1→28.88 Å / SU ML: 0.44 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.81 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.289 902 5.05 %
Rwork0.272 --
obs0.273 17877 86.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.1→28.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5394 0 50 0 5444
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0115519
X-RAY DIFFRACTIONf_angle_d1.6687494
X-RAY DIFFRACTIONf_dihedral_angle_d16.3911888
X-RAY DIFFRACTIONf_chiral_restr0.089906
X-RAY DIFFRACTIONf_plane_restr0.01953
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1003-3.29430.3744790.331355X-RAY DIFFRACTION43
3.2943-3.54820.34481410.31792486X-RAY DIFFRACTION78
3.5482-3.90450.33491710.29353240X-RAY DIFFRACTION100
3.9045-4.46770.27091730.26353231X-RAY DIFFRACTION100
4.4677-5.62210.26791770.25293258X-RAY DIFFRACTION100
5.6221-28.88430.25521610.25723405X-RAY DIFFRACTION100

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