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- PDB-8f0w: Tudor Domain of Tumor suppressor p53BP1 with MFP-5956 -

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Basic information

Entry
Database: PDB / ID: 8f0w
TitleTudor Domain of Tumor suppressor p53BP1 with MFP-5956
ComponentsTP53-binding protein 1
KeywordsTRANSCRIPTION / 53BP1 / Tudor / MFP-5956 / 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 / DNA damage checkpoint signaling / replication fork / Nonhomologous End-Joining (NHEJ) / positive regulation of DNA-binding transcription factor activity / transcription coregulator activity / G2/M DNA damage checkpoint / protein homooligomerization / kinetochore / 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 / damaged DNA binding / chromosome, telomeric region / 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
Tumour suppressor p53-binding protein-1 Tudor domain / : / Tumour suppressor p53-binding protein-1 Tudor / BRCA1 C Terminus (BRCT) domain / : / : / breast cancer carboxy-terminal domain / BRCT domain profile. / BRCT domain / BRCT domain superfamily / Ribosomal protein L2, domain 2
Similarity search - Domain/homology
Chem-X9N / TP53-binding protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.52 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)
Funding support1items
OrganizationGrant numberCountry
Other private
CitationJournal: to be published
Title: Tudor Domain of Tumor suppressor p53BP1 with MFP-5956
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
DepositionNov 4, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 18, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)28,80139
Polymers28,2442
Non-polymers55737
Water5,008278
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.479, 77.027, 87.208
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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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-X9N / 1-[4-(4-ethylpiperazin-1-yl)-3-fluorophenyl]butan-1-one


Mass: 278.365 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H23FN2O / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical...
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 35 / Source method: obtained synthetically
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 278 / 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: 2.88 Å3/Da / Density % sol: 57.33 % / Mosaicity: 0.861 °
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: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.54 Å
DetectorType: RIGAKU SATURN A200 / Detector: CCD / Date: Feb 26, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.52→50.01 Å / Num. obs: 48449 / % possible obs: 94.7 % / Redundancy: 7.5 % / Rmerge(I) obs: 0.036 / Rpim(I) all: 0.014 / Rrim(I) all: 0.039 / Χ2: 1.004 / Net I/σ(I): 15.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.52-1.555.50.44419740.8310.1980.4890.76779.1
1.55-1.576.50.35123160.9220.1470.3820.62290.8
1.57-1.67.10.28923140.9590.1150.3120.5992.7
1.6-1.647.20.24123490.9730.0950.2590.6292.5
1.64-1.677.20.20523300.9810.0810.2210.64292.4
1.67-1.717.30.17523820.9840.0690.1890.65594
1.71-1.757.40.15423620.9880.060.1650.71393.9
1.75-1.87.40.12223790.9920.0470.1310.79193.7
1.8-1.867.50.10624110.9940.0410.1130.84395.3
1.86-1.927.60.08723940.9960.0330.0940.90995
1.92-1.987.70.07124230.9970.0270.0760.95295.5
1.98-2.067.80.06124470.9980.0230.0651.11695.9
2.06-2.167.90.05224530.9980.0190.0551.14996.5
2.16-2.2780.04824850.9990.0180.0511.19496.9
2.27-2.4180.04324760.9990.0160.0461.17996.7
2.41-2.67.90.03825090.9990.0140.041.14598
2.6-2.867.90.03425630.9990.0130.0361.19698
2.86-3.277.90.0325490.9990.0110.0331.42498.8
3.27-4.137.80.02826130.9990.0110.031.54699.2
4.13-507.10.02727200.9990.010.0291.48697.7

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation4.03 Å19.88 Å
Translation4.03 Å19.88 Å

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Processing

Software
NameVersionClassification
HKL-3000data scaling
PHASER2.8.2phasing
REFMAC5.8.0189refinement
PDB_EXTRACT3.27data extraction
HKL-3000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2G3R

2g3r


Resolution: 1.52→50.01 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.947 / SU B: 1.28 / SU ML: 0.048 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.081 / ESU R Free: 0.081 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2344 944 2 %RANDOM
Rwork0.2117 ---
obs0.2122 47357 94.65 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 53.88 Å2 / Biso mean: 22.762 Å2 / Biso min: 14.35 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2--0.33 Å2-0 Å2
3----0.32 Å2
Refinement stepCycle: final / Resolution: 1.52→50.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1928 0 75 279 2282
Biso mean--25.99 32.6 -
Num. residues----242
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0192093
X-RAY DIFFRACTIONr_bond_other_d0.0020.021970
X-RAY DIFFRACTIONr_angle_refined_deg1.4291.9672827
X-RAY DIFFRACTIONr_angle_other_deg0.90534573
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3635259
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.83723.64696
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.10215376
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.6711514
X-RAY DIFFRACTIONr_chiral_restr0.0840.2290
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022421
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02457
LS refinement shellResolution: 1.52→1.559 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.361 61 -
Rwork0.392 3026 -
all-3087 -
obs--83.03 %

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