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- PDB-6va5: Tudor Domain of Tumor suppressor p53BP1 with MFP-4184 -

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Basic information

Entry
Database: PDB / ID: 6va5
TitleTudor Domain of Tumor suppressor p53BP1 with MFP-4184
ComponentsTP53-binding protein 1
KeywordsTRANSCRIPTION / 53BP1 / Tudor / MFP-4184 / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


ubiquitin-modified histone reader activity / positive regulation of isotype switching / cellular response to X-ray / double-strand break repair via classical nonhomologous end joining / DNA repair complex / negative regulation of double-strand break repair via homologous recombination / telomeric DNA binding / SUMOylation of transcription factors / methylated histone binding / histone reader activity ...ubiquitin-modified histone reader activity / positive regulation of isotype switching / cellular response to X-ray / double-strand break repair via classical nonhomologous end joining / DNA repair complex / negative regulation of double-strand break repair via homologous recombination / telomeric DNA binding / SUMOylation of transcription factors / methylated histone binding / histone reader activity / replication fork / DNA damage checkpoint signaling / transcription coregulator activity / Nonhomologous End-Joining (NHEJ) / G2/M DNA damage checkpoint / protein homooligomerization / kinetochore / double-strand break repair via nonhomologous end joining / positive regulation of DNA-binding transcription factor activity / p53 binding / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / site of double-strand break / Processing of DNA double-strand break ends / histone binding / RNA polymerase II-specific DNA-binding transcription factor binding / chromosome, telomeric region / damaged DNA binding / nuclear body / DNA damage response / positive regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
: / BRCA1 C Terminus (BRCT) domain / Tumour suppressor p53-binding protein-1 Tudor domain / Tumour suppressor p53-binding protein-1 Tudor / : / : / SH3 type barrels. - #30 / SH3 type barrels. - #140 / breast cancer carboxy-terminal domain / BRCT domain profile. ...: / BRCA1 C Terminus (BRCT) domain / Tumour suppressor p53-binding protein-1 Tudor domain / Tumour suppressor p53-binding protein-1 Tudor / : / : / SH3 type barrels. - #30 / SH3 type barrels. - #140 / breast cancer carboxy-terminal domain / BRCT domain profile. / BRCT domain / BRCT domain superfamily / SH3 type barrels. / Ribosomal protein L2, domain 2 / Roll / Mainly Beta
Similarity search - Domain/homology
2-(4-methylpiperazin-1-yl)aniline / TP53-binding protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.28 Å
AuthorsZeng, H. / Dong, A. / Headey, S. / Gunzburg, M. / Doak, B. / James, L.I. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Brown, P.J. / Structural Genomics Consortium (SGC)
CitationJournal: to be published
Title: Tudor Domain of Tumor suppressor p53BP1 with MFP-4184
Authors: Zeng, H. / Dong, A. / Headey, S. / Gunzburg, M. / Doak, B. / James, L.I. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Brown, P.J. / Structural Genomics Consortium (SGC)
History
DepositionDec 16, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 29, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TP53-binding protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,79010
Polymers14,1221
Non-polymers6689
Water2,558142
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.678, 44.822, 65.542
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein TP53-binding protein 1 / p53BP1


Mass: 14121.893 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TP53BP1 / Plasmid: pET28-MHL / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): -V2R-pRARE2 / References: UniProt: Q12888

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Non-polymers , 5 types, 151 molecules

#2: Chemical ChemComp-QSS / 2-(4-methylpiperazin-1-yl)aniline


Mass: 191.273 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H17N3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 3 / Source method: obtained synthetically
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 142 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.22 Å3/Da / Density % sol: 44.58 % / Mosaicity: 0.536 °
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 2M ammonium sulfate, 0.1 M HEPES pH 7.5, 2% PEG 400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Feb 1, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.28→50 Å / Num. obs: 33389 / % possible obs: 99.9 % / Redundancy: 6.4 % / Rmerge(I) obs: 0.101 / Rpim(I) all: 0.042 / Rrim(I) all: 0.11 / Χ2: 0.859 / Net I/σ(I): 6.2 / Num. measured all: 214888
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.28-1.34.60.81816460.6930.4090.9190.51999.9
1.3-1.335.20.72316570.8540.3450.8040.55599.8
1.33-1.355.20.69316240.7870.3260.7690.53899.1
1.35-1.3860.72316330.8040.3220.7930.52999.8
1.38-1.416.20.66516380.8850.2890.7260.51799.9
1.41-1.446.30.57616590.8970.2480.6280.556100
1.44-1.486.20.51416420.8970.2240.5620.535100
1.48-1.526.70.46616380.9380.1950.5060.592100
1.52-1.566.70.37516540.9540.1570.4080.612100
1.56-1.616.70.33116580.9670.1380.360.64499.9
1.61-1.677.10.28616510.9730.1150.3090.654100
1.67-1.7470.22416690.9790.0910.2420.673100
1.74-1.826.70.17216490.9880.0720.1870.704100
1.82-1.917.10.14716600.9910.0590.1590.809100
1.91-2.036.70.11416810.9930.0480.1231.007100
2.03-2.197.30.0916770.9960.0360.0971.128100
2.19-2.4170.08516850.9940.0340.0911.276100
2.41-2.766.90.0717080.9960.0290.0761.199100
2.76-3.476.80.05717310.9980.0240.0621.60699.9
3.47-506.40.05518290.9970.0240.061.93499.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
SCALEPACKdata scaling
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4RG2

4rg2


Resolution: 1.28→37 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.966 / SU B: 0.733 / SU ML: 0.032 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.048 / ESU R Free: 0.047
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1849 1227 3.7 %RANDOM
Rwork0.1738 ---
obs0.1743 31860 99.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 58.87 Å2 / Biso mean: 13.412 Å2 / Biso min: 6.54 Å2
Baniso -1Baniso -2Baniso -3
1-0.62 Å2-0 Å20 Å2
2---0.48 Å20 Å2
3----0.14 Å2
Refinement stepCycle: final / Resolution: 1.28→37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms981 0 43 147 1171
Biso mean--18.19 23.73 -
Num. residues----123
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0191114
X-RAY DIFFRACTIONr_bond_other_d0.0020.021034
X-RAY DIFFRACTIONr_angle_refined_deg1.3961.9761507
X-RAY DIFFRACTIONr_angle_other_deg0.88332396
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3225138
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.58322.74551
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.53515198
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.2321510
X-RAY DIFFRACTIONr_chiral_restr0.0880.2154
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021280
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02254
LS refinement shellResolution: 1.28→1.313 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.213 67 -
Rwork0.27 2324 -
all-2391 -
obs--99.87 %

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