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- PDB-6hm4: Crystal structure of Rad4 BRCT1,2 in complex with a Mdb1 phosphop... -

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Basic information

Entry
Database: PDB / ID: 6hm4
TitleCrystal structure of Rad4 BRCT1,2 in complex with a Mdb1 phosphopeptide
Components
  • DNA damage response protein Mdb1
  • S-M checkpoint control protein rad4
KeywordsCELL CYCLE / BRCT domain phosphopeptide recognition
Function / homology
Function and homology information


mitotic DNA damage checkpoint signaling / mitotic spindle pole body / mitotic spindle midzone / DNA replication preinitiation complex / mitotic DNA replication checkpoint signaling / nuclear replication fork / mitotic G2 DNA damage checkpoint signaling / DNA replication initiation / signaling adaptor activity / mitotic spindle ...mitotic DNA damage checkpoint signaling / mitotic spindle pole body / mitotic spindle midzone / DNA replication preinitiation complex / mitotic DNA replication checkpoint signaling / nuclear replication fork / mitotic G2 DNA damage checkpoint signaling / DNA replication initiation / signaling adaptor activity / mitotic spindle / site of double-strand break / chromatin / nucleus / cytosol / cytoplasm
Similarity search - Function
twin BRCT domain / BRCT domain / BRCA1 C Terminus (BRCT) domain / breast cancer carboxy-terminal domain / BRCT domain profile. / BRCT domain / BRCT domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / DNA damage response protein Mdb1 / S-M checkpoint control protein rad4
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.77018592355 Å
AuthorsDay, M. / Rappas, M. / Oliver, A.W. / Pearl, L.H.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Cancer Research UKC302/A14532 United Kingdom
CitationJournal: Elife / Year: 2018
Title: BRCT domains of the DNA damage checkpoint proteins TOPBP1/Rad4 display distinct specificities for phosphopeptide ligands.
Authors: Day, M. / Rappas, M. / Ptasinska, K. / Boos, D. / Oliver, A.W. / Pearl, L.H.
History
DepositionSep 12, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 17, 2018Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: S-M checkpoint control protein rad4
B: DNA damage response protein Mdb1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,1124
Polymers22,9912
Non-polymers1212
Water5,188288
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1290 Å2
ΔGint-5 kcal/mol
Surface area10300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.170, 40.000, 54.960
Angle α, β, γ (deg.)90.000, 105.160, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein S-M checkpoint control protein rad4 / P74 / Protein cut5


Mass: 21286.475 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (strain 972 / ATCC 24843) (yeast)
Strain: 972 / ATCC 24843 / Gene: rad4, cut5, SPAC23C4.18c / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P32372
#2: Protein/peptide DNA damage response protein Mdb1 / BRCT domain protein Mdb1 / Midzone and DNA break-localizing protein 1


Mass: 1704.857 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Schizosaccharomyces pombe (fission yeast) / References: UniProt: O14079
#3: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 288 / 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: 2.43 Å3/Da / Density % sol: 49.35 %
Crystal growTemperature: 287.15 K / Method: vapor diffusion, sitting drop
Details: 200 mM Sodium acetate trihydrate, 100 mM Tris 8.5 and 30 % w/v PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 11, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.77→31.94 Å / Num. obs: 19339 / % possible obs: 93.07 % / Redundancy: 2.6 % / Biso Wilson estimate: 20.48 Å2 / Net I/σ(I): 16.52
Reflection shellResolution: 1.77→1.833 Å

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
xia2data reduction
Aimlessdata scaling
PHASERphasing
RefinementResolution: 1.77018592355→31.9379091525 Å / SU ML: 0.232410282223 / Cross valid method: FREE R-VALUE / σ(F): 1.36458498044 / Phase error: 22.5724322855
RfactorNum. reflection% reflection
Rfree0.211405870627 991 5.1246250905 %
Rwork0.166370856717 --
obs0.16857933455 19338 93.083032491 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 22.6342605533 Å2
Refinement stepCycle: LAST / Resolution: 1.77018592355→31.9379091525 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1531 0 8 288 1827
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006478079138321595
X-RAY DIFFRACTIONf_angle_d0.8334057742592167
X-RAY DIFFRACTIONf_chiral_restr0.0515908156085242
X-RAY DIFFRACTIONf_plane_restr0.00542070517148272
X-RAY DIFFRACTIONf_dihedral_angle_d4.707474504181299
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7702-1.86350.3554132945821280.2752398766252010X-RAY DIFFRACTION72.3274695535
1.8635-1.98020.2560246568871400.2093214939972555X-RAY DIFFRACTION91.6666666667
1.9802-2.13310.2384890264761390.1738189521472748X-RAY DIFFRACTION98.2306907111
2.1331-2.34770.2275240409131560.1607466581942744X-RAY DIFFRACTION98.4051577876
2.3477-2.68730.21508082081390.1650501571952775X-RAY DIFFRACTION98.147524419
2.6873-3.38510.1967984848691450.1585111396412754X-RAY DIFFRACTION97.1514745308
3.3851-31.94310.1774916306841440.1520049919252761X-RAY DIFFRACTION95.6221198157

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