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- PDB-7p0l: Crystal structure of S.pombe Mdb1 BRCT domains in complex with a ... -

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Basic information

Entry
Database: PDB / ID: 7p0l
TitleCrystal structure of S.pombe Mdb1 BRCT domains in complex with a H2A phosphopeptide
Components
  • DNA damage response protein Mdb1
  • Histone H2A-beta
KeywordsSIGNALING PROTEIN / DNA damage response
Function / homology
Function and homology information


Condensation of Prophase Chromosomes / : / : / Assembly of the ORC complex at the origin of replication / Oxidative Stress Induced Senescence / RMTs methylate histone arginines / Ub-specific processing proteases / HDACs deacetylate histones / Estrogen-dependent gene expression / RNA Polymerase I Promoter Escape ...Condensation of Prophase Chromosomes / : / : / Assembly of the ORC complex at the origin of replication / Oxidative Stress Induced Senescence / RMTs methylate histone arginines / Ub-specific processing proteases / HDACs deacetylate histones / Estrogen-dependent gene expression / RNA Polymerase I Promoter Escape / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / Transcriptional regulation by small RNAs / mating-type region heterochromatin / mitotic DNA damage checkpoint signaling / chromosome, subtelomeric region / mitotic spindle midzone / homologous chromosome segregation / rDNA heterochromatin / mitotic chromosome condensation / chromatin-protein adaptor activity / mitotic G2 DNA damage checkpoint signaling / pericentric heterochromatin / structural constituent of chromatin / heterochromatin formation / nucleosome / double-strand break repair / site of double-strand break / protein heterodimerization activity / DNA binding / 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 / Histone H2A conserved site / Histone H2A signature. / Histone H2A, C-terminal domain ...: / BRCT domain / BRCA1 C Terminus (BRCT) domain / breast cancer carboxy-terminal domain / BRCT domain profile. / BRCT domain / BRCT domain superfamily / Histone H2A conserved site / Histone H2A signature. / Histone H2A, C-terminal domain / C-terminus of histone H2A / Histone 2A / Histone H2A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 domain / Histone-fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
DNA damage response protein Mdb1 / Histone H2A-beta
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.97 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 1.0Dec 1, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA damage response protein Mdb1
B: DNA damage response protein Mdb1
C: Histone H2A-beta
D: Histone H2A-beta


Theoretical massNumber of molelcules
Total (without water)47,8764
Polymers47,8764
Non-polymers00
Water2,864159
1
A: DNA damage response protein Mdb1
C: Histone H2A-beta


Theoretical massNumber of molelcules
Total (without water)23,9382
Polymers23,9382
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area850 Å2
ΔGint-9 kcal/mol
Surface area10440 Å2
MethodPISA
2
B: DNA damage response protein Mdb1
D: Histone H2A-beta


Theoretical massNumber of molelcules
Total (without water)23,9382
Polymers23,9382
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area790 Å2
ΔGint-7 kcal/mol
Surface area10060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.380, 42.050, 96.290
Angle α, β, γ (deg.)90.000, 91.870, 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
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:

Ens-ID: 1 / Beg auth comp-ID: THR / Beg label comp-ID: THR / End auth comp-ID: ASP / End label comp-ID: ASP / Auth seq-ID: 387 - 581 / Label seq-ID: 5 - 199

Dom-IDComponent-IDSelection detailsAuth asym-IDLabel asym-ID
11(chain 'A' and (resid 387 through 404 or (resid 405...AA
22(chain 'B' and (resid 387 through 507 or (resid 508...BB

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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.: 2
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: Protein/peptide Histone H2A-beta / H2A.2


Mass: 1241.246 Da / Num. of mol.: 2 / Source method: obtained synthetically
Source: (synth.) Schizosaccharomyces pombe (strain 972 / ATCC 24843) (yeast)
References: UniProt: P04910
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 159 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 1.73 Å3/Da / Density % sol: 28.93 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 200mM Magnesium Chloride 100mM TRIS pH 8.0 30% (w/v) PEG 4000

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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: 1.97→48.12 Å / Num. obs: 23405 / % possible obs: 98.7 % / Redundancy: 3.2 % / Biso Wilson estimate: 35.94 Å2 / Rpim(I) all: 0.044 / Net I/σ(I): 1.087
Reflection shellResolution: 1.97→2.02 Å / Num. unique obs: 1720 / Rpim(I) all: 0.383

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
xia2data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7P0J

7p0j


Resolution: 1.97→48.12 Å / SU ML: 0.2648 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.0307
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2467 1158 4.95 %
Rwork0.2078 22234 -
obs0.2098 23392 98.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 48.47 Å2
Refinement stepCycle: LAST / Resolution: 1.97→48.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3125 0 0 159 3284
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00473173
X-RAY DIFFRACTIONf_angle_d0.81864289
X-RAY DIFFRACTIONf_chiral_restr0.0499499
X-RAY DIFFRACTIONf_plane_restr0.0059547
X-RAY DIFFRACTIONf_dihedral_angle_d18.29731178
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.97-2.060.3521420.27242758X-RAY DIFFRACTION99.28
2.06-2.170.29011440.25582752X-RAY DIFFRACTION98.47
2.17-2.30.32631420.23352735X-RAY DIFFRACTION97.66
2.3-2.480.27171820.2132748X-RAY DIFFRACTION99.66
2.48-2.730.29381030.20642826X-RAY DIFFRACTION99.32
2.73-3.130.24261440.21412816X-RAY DIFFRACTION99.46
3.13-3.940.23331290.19162787X-RAY DIFFRACTION97.82
3.94-48.120.21961720.19882812X-RAY DIFFRACTION97.14

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