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- PDB-7p0j: Crystal structure of S.pombe Mdb1 BRCT domains -

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Basic information

Entry
Database: PDB / ID: 7p0j
TitleCrystal structure of S.pombe Mdb1 BRCT domains
ComponentsDNA damage response protein Mdb1
KeywordsSIGNALING PROTEIN / DNA damage response
Function / homology
Function and homology information


mitotic spindle midzone / mitotic G2 DNA damage checkpoint signaling / site of double-strand break / nucleus / cytoplasm
Similarity search - Function
: / 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
CITRIC ACID / DNA damage response protein Mdb1
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.48 Å
AuthorsDay, M. / Oliver, A.W. / Pearl, L.H.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Cancer Research UKC302/A14532 United Kingdom
Cancer Research UKC302/A24386 United Kingdom
Citation
Journal: DNA Repair (Amst) / Year: 2021
Title: Phosphorylation-dependent assembly of DNA damage response systems and the central roles of TOPBP1.
Authors: Day, M. / Oliver, A.W. / Pearl, L.H.
#1: Journal: Acta Crystallogr., Sect. D: Biol. Crystallogr. / Year: 2012
Title: Towards automated crystallographic structure refinement with phenix.refine.
Authors: Afonine, P.V.
History
DepositionJun 29, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 13, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA damage response protein Mdb1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,9595
Polymers22,6971
Non-polymers2624
Water5,152286
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area600 Å2
ΔGint-23 kcal/mol
Surface area10660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.180, 44.120, 49.860
Angle α, β, γ (deg.)90.000, 92.370, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11A-602-

NA

21A-604-

MG

31A-723-

HOH

41A-914-

HOH

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Components

#1: Protein DNA damage response protein Mdb1 / BRCT domain protein Mdb1 / Midzone and DNA break-localizing protein 1


Mass: 22696.945 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: mdb1, SPAC2E11.14, SPACUNK4.14 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O14079
#2: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 286 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.76 Å3/Da / Density % sol: 55.5 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 0.2 M sodium citrate 0.1 M Bis Tris propane 7.5 20 % w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97957 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 11, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97957 Å / Relative weight: 1
ReflectionResolution: 1.48→49.82 Å / Num. obs: 41143 / % possible obs: 99.1 % / Redundancy: 3.2 % / Biso Wilson estimate: 17.83 Å2 / Rpim(I) all: 0.036 / Net I/σ(I): 1.306
Reflection shellResolution: 1.48→1.52 Å / Num. unique obs: 3071 / Rpim(I) all: 0.519

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
xia2data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 1.48→49.82 Å / SU ML: 0.1413 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.3295
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1965 2009 4.88 %
Rwork0.1703 39132 -
obs0.1715 41141 98.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 22.27 Å2
Refinement stepCycle: LAST / Resolution: 1.48→49.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1559 0 16 286 1861
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01151665
X-RAY DIFFRACTIONf_angle_d1.09182262
X-RAY DIFFRACTIONf_chiral_restr0.0844256
X-RAY DIFFRACTIONf_plane_restr0.0068294
X-RAY DIFFRACTIONf_dihedral_angle_d20.2096652
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.48-1.520.28431340.26592823X-RAY DIFFRACTION99.33
1.52-1.560.25811320.23242775X-RAY DIFFRACTION99.32
1.56-1.60.24151300.20992798X-RAY DIFFRACTION99.66
1.6-1.660.26311400.20262811X-RAY DIFFRACTION99.66
1.66-1.710.21351530.19342789X-RAY DIFFRACTION99.53
1.71-1.780.20611540.1862797X-RAY DIFFRACTION99.8
1.78-1.860.21271460.1822783X-RAY DIFFRACTION99.63
1.86-1.960.21331440.17922770X-RAY DIFFRACTION98.71
1.96-2.090.19131570.16682809X-RAY DIFFRACTION99.53
2.09-2.250.18381400.15942768X-RAY DIFFRACTION98.71
2.25-2.470.18121510.15042775X-RAY DIFFRACTION98.12
2.47-2.830.18581410.15942794X-RAY DIFFRACTION98.59
2.83-3.570.19111420.16552791X-RAY DIFFRACTION97.8
3.57-49.820.18511450.16232849X-RAY DIFFRACTION97.3

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