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- PDB-6upt: Tudor Domain of Tumor suppressor p53BP1 with MFP-2706 -

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Basic information

Entry
Database: PDB / ID: 6upt
TitleTudor Domain of Tumor suppressor p53BP1 with MFP-2706
ComponentsTP53-binding protein 1
KeywordsPROTEIN BINDING / 53BP1 / Tudor / MFP-2706 / 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 / protein localization to site of double-strand break / DNA repair complex / telomeric DNA binding / SUMOylation of transcription factors / negative regulation of double-strand break repair via homologous recombination / methylated histone binding ...ubiquitin-modified histone reader activity / positive regulation of isotype switching / cellular response to X-ray / double-strand break repair via classical nonhomologous end joining / protein localization to site of double-strand break / DNA repair complex / telomeric DNA binding / SUMOylation of transcription factors / negative regulation of double-strand break repair via homologous recombination / methylated histone binding / histone reader activity / replication fork / DNA damage checkpoint signaling / Nonhomologous End-Joining (NHEJ) / transcription coregulator activity / G2/M DNA damage checkpoint / protein homooligomerization / kinetochore / positive regulation of DNA-binding transcription factor activity / double-strand break repair via nonhomologous end joining / 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-((2-chlorobenzyl)thio)-4,5-dihydro-1H-imidazole / Tumor protein p53 binding protein 1 / TP53-binding protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.96 Å
AuthorsThe, J. / 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-2706
Authors: The, J. / 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
DepositionOct 18, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 20, 2019Provider: 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
B: TP53-binding protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,3568
Polymers28,1302
Non-polymers2276
Water1,60389
1
A: TP53-binding protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,2925
Polymers14,0651
Non-polymers2274
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: TP53-binding protein 1


Theoretical massNumber of molelcules
Total (without water)14,0653
Polymers14,0651
Non-polymers02
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)125.050, 125.050, 125.050
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number199
Space group name H-MI213
DetailsTHE AUTHOR STATES THAT THE BIOLOGICAL UNIT OF THIS PROTEIN IS UNKNOWN.

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Components

#1: Protein TP53-binding protein 1


Mass: 14064.842 Da / Num. of mol.: 2
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: A6NNK5, UniProt: Q12888*PLUS
#2: Chemical ChemComp-QFM / 2-((2-chlorobenzyl)thio)-4,5-dihydro-1H-imidazole / 2-{[(2-chlorophenyl)methyl]sulfanyl}-4,5-dihydro-1H-imidazole


Mass: 226.726 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H11ClN2S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 5 / Source method: obtained synthetically
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 89 / Source method: isolated from a natural source / Formula: H2O
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: 2.9 Å3/Da / Density % sol: 57.54 % / Mosaicity: 0.317 °
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: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 9, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.96→40 Å / Num. obs: 23455 / % possible obs: 100 % / Redundancy: 10.8 % / Rmerge(I) obs: 0.056 / Rpim(I) all: 0.018 / Rrim(I) all: 0.058 / Χ2: 0.716 / Net I/σ(I): 8.8 / Num. measured all: 252961
Reflection shell

Diffraction-ID: 1 / % possible all: 100

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2
1.96-1.9910.10.9511420.7290.3141.0020.595
1.99-2.0310.80.77811810.8450.2470.8170.617
2.03-2.0711.20.6311470.8910.1960.6610.636
2.07-2.1111.10.53311450.9120.1670.5590.633
2.11-2.1610.90.41711900.9560.1320.4380.649
2.16-2.2110.90.36911470.960.1170.3870.644
2.21-2.2610.60.30311620.9740.0980.3190.661
2.26-2.329.80.26411590.9750.0890.2790.66
2.32-2.399.70.21911670.9840.0740.2310.679
2.39-2.4711.20.1911800.990.0590.1990.706
2.47-2.5611.60.16311470.9920.050.170.693
2.56-2.6611.50.13712010.9960.0420.1440.699
2.66-2.7811.30.1111610.9970.0340.1150.731
2.78-2.9311.10.07811700.9980.0240.0820.785
2.93-3.1110.70.05911630.9990.0190.0620.791
3.11-3.359.80.04511830.9990.0150.0480.831
3.35-3.6910.40.03811880.9990.0120.040.86
3.69-4.2211.70.03211800.9990.010.0330.854
4.22-5.3211.20.029119710.0090.030.801
5.32-4010.10.0312450.9990.010.0320.767

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
REFMAC5.8.0253refinement
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 4RG2

4rg2


Resolution: 1.96→39.58 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.931 / SU B: 3.927 / SU ML: 0.111 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.162 / ESU R Free: 0.15
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2556 1189 5.1 %RANDOM
Rwork0.2223 ---
obs0.2238 22255 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 104.5 Å2 / Biso mean: 40.417 Å2 / Biso min: 21.16 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: final / Resolution: 1.96→39.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1808 0 19 90 1917
Biso mean--56.31 45.29 -
Num. residues----239
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0131883
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171698
X-RAY DIFFRACTIONr_angle_refined_deg1.4611.642544
X-RAY DIFFRACTIONr_angle_other_deg1.3261.5923888
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.0275241
X-RAY DIFFRACTIONr_dihedral_angle_2_deg26.52820.53893
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.02515295
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.5071514
X-RAY DIFFRACTIONr_chiral_restr0.0650.2225
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022216
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02448
LS refinement shellResolution: 1.961→2.011 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.302 88 -
Rwork0.28 1625 -
all-1713 -
obs--100 %

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