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- PDB-6vip: TUDOR DOMAIN OF TUMOR SUPPRESSOR P53BP1 WITH MFP-6008 -

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Basic information

Entry
Database: PDB / ID: 6vip
TitleTUDOR DOMAIN OF TUMOR SUPPRESSOR P53BP1 WITH MFP-6008
ComponentsTP53-binding protein 1
KeywordsTRANSCRIPTION / 53BP1 / Tudor / MFP-6008 / Structural Genomics / Structural Genomics Consortium / SGC / PROTEIN BINDING
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
Chem-QXY / TP53-binding protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.36 Å
AuthorsThe, J. / Hong, Z. / Dong, A. / Headey, S. / Gunzburg, M. / Doak, B. / James, L.I. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. ...The, J. / Hong, Z. / 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-6008
Authors: The, J. / Hong, Z. / 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
DepositionJan 13, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 12, 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
B: TP53-binding protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,8978
Polymers28,2442
Non-polymers6536
Water2,810156
1
A: TP53-binding protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,4484
Polymers14,1221
Non-polymers3263
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: TP53-binding protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,4484
Polymers14,1221
Non-polymers3263
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)57.887, 60.156, 69.721
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
DetailsTHE AUTHOR STATES THAT THE BIOLOGICAL UNIT OF THIS PROTEIN IS UNKNOWN.

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Components

#1: Protein TP53-binding protein 1 / p53BP1


Mass: 14121.893 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) / Variant (production host): -V2R-pRARE2 / References: UniProt: Q12888
#2: Chemical ChemComp-QXY / {4-[(3,5-dimethyl-1H-pyrazol-1-yl)methyl]phenyl}(4-ethylpiperazin-1-yl)methanone


Mass: 326.436 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H26N4O / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-UNX / UNKNOWN ATOM OR ION


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


Mass: 18.015 Da / Num. of mol.: 156 / 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: 2.15 Å3/Da / Density % sol: 42.76 % / Mosaicity: 0.404 °
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: 1.36→50 Å / Num. obs: 52885 / % possible obs: 100 % / Redundancy: 7.7 % / Rmerge(I) obs: 0.063 / Rpim(I) all: 0.025 / Rrim(I) all: 0.068 / Χ2: 0.942 / Net I/σ(I): 7.9 / Num. measured all: 406505
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.36-1.387.50.80425970.8230.3130.8640.448100
1.38-1.417.30.68826200.8440.2720.7420.434100
1.41-1.447.80.58626310.8820.2240.6280.432100
1.44-1.477.40.49425970.9110.1930.5310.442100
1.47-1.57.80.38225760.9450.1450.4090.452100
1.5-1.537.90.32426580.9610.1220.3470.477100
1.53-1.577.80.25525920.9750.0970.2730.479100
1.57-1.617.50.21526110.9790.0840.2310.49100
1.61-1.667.60.18726170.9840.0720.2010.506100
1.66-1.717.80.15126230.9890.0580.1620.543100
1.71-1.777.50.12526370.9910.0490.1340.599100
1.77-1.8580.10326240.9940.0390.110.683100
1.85-1.937.90.08526450.9950.0320.0910.803100
1.93-2.037.50.0726120.9960.0270.0750.972100
2.03-2.1680.06326510.9960.0240.0681.221100
2.16-2.337.70.0626760.9970.0230.0641.373100
2.33-2.568.10.05826530.9970.0220.0621.556100
2.56-2.937.60.05526820.9970.0210.0591.743100
2.93-3.697.70.05327200.9970.020.0572.28699.9
3.69-507.20.05428630.9970.0210.0582.72799.8

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3.66 Å19.98 Å
Translation3.66 Å19.98 Å

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PHASER2.7.17phasing
REFMAC5.8.0258refinement
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4RG2

4rg2


Resolution: 1.36→45.55 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.963 / SU B: 1.051 / SU ML: 0.043 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.061 / ESU R Free: 0.059
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2106 1274 2.4 %RANDOM
Rwork0.1992 ---
obs0.1995 51545 99.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 64.94 Å2 / Biso mean: 21.602 Å2 / Biso min: 10.97 Å2
Baniso -1Baniso -2Baniso -3
1--0.41 Å2-0 Å20 Å2
2--0.65 Å2-0 Å2
3----0.24 Å2
Refinement stepCycle: final / Resolution: 1.36→45.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1886 0 52 159 2097
Biso mean--34.72 29.35 -
Num. residues----241
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0132021
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171857
X-RAY DIFFRACTIONr_angle_refined_deg1.571.6292730
X-RAY DIFFRACTIONr_angle_other_deg1.3981.6254300
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.275249
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.08121.91999
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.28115339
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.8371513
X-RAY DIFFRACTIONr_chiral_restr0.0770.2236
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022430
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02454
LS refinement shellResolution: 1.361→1.396 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.262 91 -
Rwork0.281 3727 -
all-3818 -
obs--98.61 %

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