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- PDB-1g6g: X-RAY STRUCTURE OF THE N-TERMINAL FHA DOMAIN FROM S. CEREVISIAE R... -

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Basic information

Entry
Database: PDB / ID: 1g6g
TitleX-RAY STRUCTURE OF THE N-TERMINAL FHA DOMAIN FROM S. CEREVISIAE RAD53P IN COMPLEX WITH A PHOSPHOTHREONINE PEPTIDE AT 1.6 A RESOLUTION
Components
  • PROTEIN KINASE RAD53
  • SER-LEU-GLU-VAL-TPO-GLU-ALA-ASPALA-THR-PHE-ALA-LYS
KeywordsCELL CYCLE / beta-sandwich / phosphopeptide complex
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 / Tumour Suppressor Smad4 - #20 / Tumour Suppressor Smad4 / 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. ...Serine/threonine-protein kinase Rad53 / Tumour Suppressor Smad4 - #20 / Tumour Suppressor Smad4 / 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 / Sandwich / Mainly Beta
Similarity search - Domain/homology
Serine/threonine-protein kinase RAD53
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.6 Å
AuthorsDurocher, D. / Taylor, I.A.
CitationJournal: Mol.Cell / Year: 2000
Title: The molecular basis of FHA domain:phosphopeptide binding specificity and implications for phospho-dependent signaling mechanisms.
Authors: Durocher, D. / Taylor, I.A. / Sarbassova, D. / Haire, L.F. / Westcott, S.L. / Jackson, S.P. / Smerdon, S.J. / Yaffe, M.B.
History
DepositionNov 6, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 13, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROTEIN KINASE RAD53
B: PROTEIN KINASE RAD53
E: SER-LEU-GLU-VAL-TPO-GLU-ALA-ASPALA-THR-PHE-ALA-LYS
F: SER-LEU-GLU-VAL-TPO-GLU-ALA-ASPALA-THR-PHE-ALA-LYS


Theoretical massNumber of molelcules
Total (without water)31,1834
Polymers31,1834
Non-polymers00
Water7,945441
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)33.191, 79.609, 131.467
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein PROTEIN KINASE RAD53


Mass: 14129.126 Da / Num. of mol.: 2 / Fragment: N-TERMINAL DOMAIN (INCLUDING FHA DOMAIN)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: RAD53 / Plasmid: PET22B / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P22216, Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor
#2: Protein/peptide SER-LEU-GLU-VAL-TPO-GLU-ALA-ASPALA-THR-PHE-ALA-LYS


Mass: 1462.472 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: THIS PEPTIDE WAS CHEMICALLY SYNTHESIZED.
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 441 / 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: 2.78 Å3/Da / Density % sol: 55.83 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: PEG 6000 MME, ammonium sulphate, sodium acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal grow
*PLUS
Temperature: 18 ℃ / Method: vapor diffusion / Details: also batch method
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
11 mMprotein1drop
210 mMsodium phosphate1drop
350 mMTris-HCl1drop
4150 mM1dropNaCl
530 %mPEG20001reservoir
60.2 Mammonium sulfate1reservoir
70.1 Msodium acetate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 30, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 1.57→15 Å / Num. all: 49794 / Num. obs: 49229 / % possible obs: 98.9 % / Observed criterion σ(I): 2 / Redundancy: 3.5 % / Biso Wilson estimate: 21 Å2 / Rmerge(I) obs: 0.068 / Net I/σ(I): 18.3
Reflection shellResolution: 1.57→1.61 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.42 / % possible all: 92.2
Reflection shell
*PLUS
% possible obs: 92.2 %

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Processing

Software
NameClassification
SOLVEphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MAD / Resolution: 1.6→15 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.244 2490 random
Rwork0.209 --
obs0.211 46615 -
all-47180 -
Displacement parametersBiso mean: 28.5 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.09201 Å0.08913 Å
Refinement stepCycle: LAST / Resolution: 1.6→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2123 0 0 441 2564
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.01
X-RAY DIFFRACTIONp_angle_d1.377
LS refinement shellResolution: 1.57→1.63 Å
RfactorNum. reflection% reflection
Rfree0.33 160 -
Rwork0.27 --
obs-3139 92 %
Software
*PLUS
Name: REFMAC / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg1.377

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