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- PDB-2g3r: Crystal Structure of 53BP1 tandem tudor domains at 1.2 A resolution -

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Basic information

Entry
Database: PDB / ID: 2g3r
TitleCrystal Structure of 53BP1 tandem tudor domains at 1.2 A resolution
ComponentsTumor suppressor p53-binding protein 1
KeywordsCELL CYCLE/TRANSCRIPTION / TANDEM TUDOR DOMAINS / CELL CYCLE-TRANSCRIPTION COMPLEX
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) / protein homooligomerization / G2/M DNA damage checkpoint / kinetochore / double-strand break repair via nonhomologous end joining / positive regulation of DNA-binding transcription factor activity / p53 binding / site of double-strand break / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / 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
TP53-binding protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.25 Å
AuthorsLee, J. / Botuyan, M.V. / Thompson, J.R. / Mer, G.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2006
Title: Structural Basis for the Methylation State-Specific Recognition of Histone H4-K20 by 53BP1 and Crb2 in DNA Repair.
Authors: Botuyan, M.V. / Lee, J. / Ward, I.M. / Kim, J.E. / Thompson, J.R. / Chen, J. / Mer, G.
History
DepositionFeb 20, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 2, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Derived calculations / Version format compliance
Revision 1.3Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tumor suppressor p53-binding protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,0412
Polymers13,9451
Non-polymers961
Water3,063170
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
A: Tumor suppressor p53-binding protein 1
hetero molecules

A: Tumor suppressor p53-binding protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,0824
Polymers27,8902
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area1570 Å2
ΔGint-36 kcal/mol
Surface area12920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.895, 77.834, 36.350
Angle α, β, γ (deg.)90.00, 121.13, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-116-

HOH

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Components

#1: Protein Tumor suppressor p53-binding protein 1 / p53-binding protein 1 / 53BP1


Mass: 13944.780 Da / Num. of mol.: 1
Fragment: Tandem tutor domains, residues 1484-1603 (SWS-Q12888)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TP53BP1 / Plasmid: pTEV / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q12888
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 170 / Source method: isolated from a natural source / Formula: H2O

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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: 2.43 Å3/Da / Density % sol: 49.31 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 2% PEG 400, 0.1MHEPES/Na, 2M ammonium sulfate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 27, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.25→26.8 Å / Num. obs: 32860

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ID 1XNI

1xni


Resolution: 1.25→26.8 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.941 / SU B: 1.756 / SU ML: 0.039 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.057 / ESU R Free: 0.065 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24146 1712 5 %RANDOM
Rwork0.19412 ---
obs0.1964 32860 93.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.886 Å2
Baniso -1Baniso -2Baniso -3
1--0.44 Å20 Å2-0.15 Å2
2--0.36 Å20 Å2
3----0.08 Å2
Refinement stepCycle: LAST / Resolution: 1.25→26.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms951 0 5 170 1126
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0221227
X-RAY DIFFRACTIONr_angle_refined_deg1.7361.9871677
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.775165
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.34623.3959
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.16715231
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4221511
X-RAY DIFFRACTIONr_chiral_restr0.120.2170
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.02980
X-RAY DIFFRACTIONr_nbd_refined0.2590.2569
X-RAY DIFFRACTIONr_nbtor_refined0.3110.2839
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2560.2174
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2310.241
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3230.224
X-RAY DIFFRACTIONr_mcbond_it1.1151.5747
X-RAY DIFFRACTIONr_mcangle_it1.84221204
X-RAY DIFFRACTIONr_scbond_it2.8773537
X-RAY DIFFRACTIONr_scangle_it4.0964.5472
LS refinement shellResolution: 1.25→1.278 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.336 80 -
Rwork0.369 1608 -
obs--61.92 %
Refinement TLS params.Method: refined / Origin x: 6.591 Å / Origin y: 0.719 Å / Origin z: 11.629 Å
111213212223313233
T-0.046 Å20.0059 Å20.0061 Å2--0.0023 Å20.0004 Å2---0.0258 Å2
L1.2207 °20.4828 °20.5216 °2-1.5968 °20.3283 °2--1.2624 °2
S0.0167 Å °-0.0563 Å °-0.0657 Å °0.0275 Å °-0.001 Å °0.0588 Å °0.0993 Å °-0.0381 Å °-0.0157 Å °

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