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- PDB-2xwc: Crystal structure of the DNA binding domain of human TP73 refined... -

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Basic information

Entry
Database: PDB / ID: 2xwc
TitleCrystal structure of the DNA binding domain of human TP73 refined at 1.8 A resolution
ComponentsTUMOUR PROTEIN P73
KeywordsDNA BINDING PROTEIN / DNA-BINDING PROTEIN
Function / homology
Function and homology information


positive regulation of lung ciliated cell differentiation / cerebrospinal fluid secretion / negative regulation of cardiac muscle cell proliferation / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / TP53 Regulates Transcription of Death Receptors and Ligands / Activation of PUMA and translocation to mitochondria / Regulation of TP53 Activity through Association with Co-factors / negative regulation of neuron differentiation / TP53 Regulates Transcription of Caspase Activators and Caspases / digestive tract morphogenesis ...positive regulation of lung ciliated cell differentiation / cerebrospinal fluid secretion / negative regulation of cardiac muscle cell proliferation / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / TP53 Regulates Transcription of Death Receptors and Ligands / Activation of PUMA and translocation to mitochondria / Regulation of TP53 Activity through Association with Co-factors / negative regulation of neuron differentiation / TP53 Regulates Transcription of Caspase Activators and Caspases / digestive tract morphogenesis / TP53 Regulates Transcription of Genes Involved in Cytochrome C Release / TP53 regulates transcription of several additional cell death genes whose specific roles in p53-dependent apoptosis remain uncertain / positive regulation of oligodendrocyte differentiation / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / positive regulation of cell size / neuron development / mismatch repair / MDM2/MDM4 family protein binding / regulation of mitotic cell cycle / release of cytochrome c from mitochondria / transcription corepressor binding / post-embryonic development / hippocampus development / protein tetramerization / kidney development / intrinsic apoptotic signaling pathway in response to DNA damage / p53 binding / cell junction / RUNX1 regulates transcription of genes involved in differentiation of HSCs / regulation of gene expression / DNA-binding transcription activator activity, RNA polymerase II-specific / DNA-binding transcription factor binding / negative regulation of neuron apoptotic process / RNA polymerase II-specific DNA-binding transcription factor binding / DNA-binding transcription factor activity, RNA polymerase II-specific / transcription cis-regulatory region binding / regulation of cell cycle / positive regulation of MAPK cascade / ciliary basal body / RNA polymerase II cis-regulatory region sequence-specific DNA binding / response to xenobiotic stimulus / inflammatory response / DNA-binding transcription factor activity / negative regulation of cell population proliferation / intracellular membrane-bounded organelle / DNA damage response / centrosome / regulation of transcription by RNA polymerase II / protein kinase binding / chromatin / positive regulation of DNA-templated transcription / Golgi apparatus / positive regulation of transcription by RNA polymerase II / nucleoplasm / metal ion binding / identical protein binding / nucleus / plasma membrane / cytosol
Similarity search - Function
Tumour protein p73, SAM domain / Immunoglobulin-like - #720 / p53 family signature. / p53, tetramerisation domain / P53 tetramerisation motif / p53, DNA-binding domain / P53 DNA-binding domain / p53 tumour suppressor family / p53-like tetramerisation domain superfamily / p53/RUNT-type transcription factor, DNA-binding domain superfamily ...Tumour protein p73, SAM domain / Immunoglobulin-like - #720 / p53 family signature. / p53, tetramerisation domain / P53 tetramerisation motif / p53, DNA-binding domain / P53 DNA-binding domain / p53 tumour suppressor family / p53-like tetramerisation domain superfamily / p53/RUNT-type transcription factor, DNA-binding domain superfamily / SAM domain (Sterile alpha motif) / p53-like transcription factor, DNA-binding / Sterile alpha motif. / Sterile alpha motif domain / Sterile alpha motif/pointed domain superfamily / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.82 Å
AuthorsCanning, P. / Zhang, Y. / Vollmar, M. / Krojer, T. / Ugochukwu, E. / Muniz, J.R.C. / von Delft, F. / Weigelt, J. / Arrowsmith, C.H. / Edwards, A.M. ...Canning, P. / Zhang, Y. / Vollmar, M. / Krojer, T. / Ugochukwu, E. / Muniz, J.R.C. / von Delft, F. / Weigelt, J. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Bullock, A.N.
CitationJournal: J.Mol.Biol. / Year: 2012
Title: Structural Basis for Aspp2 Recognition by the Tumor Suppressor P73.
Authors: Canning, P. / von Delft, F. / Bullock, A.N.
History
DepositionNov 3, 2010Deposition site: PDBE / Processing site: PDBE
SupersessionNov 17, 2010ID: 2XIP
Revision 1.0Nov 17, 2010Provider: repository / Type: Initial release
Revision 1.1Sep 26, 2012Group: Database references / Non-polymer description ...Database references / Non-polymer description / Structure summary / Version format compliance
Revision 1.2Apr 3, 2013Group: Database references
Revision 1.3Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.4May 1, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TUMOUR PROTEIN P73
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,7295
Polymers23,3431
Non-polymers3864
Water3,153175
1
A: TUMOUR PROTEIN P73
hetero molecules

A: TUMOUR PROTEIN P73
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,45710
Polymers46,6852
Non-polymers7728
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation14_555-y+1/4,-x+1/4,-z+1/41
Buried area2470 Å2
ΔGint-103.8 kcal/mol
Surface area21440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.370, 110.370, 110.370
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number212
Space group name H-MP4332

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Components

#1: Protein TUMOUR PROTEIN P73 / P53-LIKE TRANSCRIPTION FACTOR / P53-RELATED PROTEIN


Mass: 23342.561 Da / Num. of mol.: 1 / Fragment: DNA-BINDING DOMAIN, RESIDUES 112-311
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PNIC-CTHF / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): R3-PRARE2 / References: UniProt: O15350
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-TAM / TRIS(HYDROXYETHYL)AMINOMETHANE


Mass: 163.215 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H17NO3 / Comment: pH buffer*YM
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 175 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, PRO 111 TO MET
Has protein modificationY
Nonpolymer detailsIDENTITY OF 2 ZN IONS CONFIRMED BY MAD EXPERIMENT. PEAKS IDENTIFIED AT ZN BINDING SITES IN ...IDENTITY OF 2 ZN IONS CONFIRMED BY MAD EXPERIMENT. PEAKS IDENTIFIED AT ZN BINDING SITES IN ANOMALOUS MAPS COLLECTED AT ZN ABSORPTION EDGE. PEAKS ARE NOT PRESENT IN MAPS COLLECTED BELOW ZN ABSORPTION EDGE.
Sequence detailsRESIDUES 312-318 ARE DUE TO CLONING. INITIATOR METHIONINE IS ENGINEERED.

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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: 2.42 Å3/Da / Density % sol: 49.13 % / Description: NONE
Crystal growDetails: 1.2M SODIUM POTASSIUM TARTRATE, 0.25% PEG MME 5000, 0.1M TRIS PH 9

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795
DetectorType: ADSC CCD / Detector: CCD / Date: May 26, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.82→49.36 Å / Num. obs: 280763 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 13.2 % / Rmerge(I) obs: 0.16 / Net I/σ(I): 11.9
Reflection shellResolution: 1.82→49.36 Å / Redundancy: 12.9 % / Rmerge(I) obs: 1.24 / Mean I/σ(I) obs: 2 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.5.0110refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 20CJ

20cj


Resolution: 1.82→49.36 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.93 / SU B: 4.788 / SU ML: 0.081 / Cross valid method: THROUGHOUT / ESU R: 0.13 / ESU R Free: 0.126 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. INITIATOR MET COULD NOT BE RESOLVED OWING TO DISORDER.
RfactorNum. reflection% reflectionSelection details
Rfree0.22824 1081 5.1 %RANDOM
Rwork0.18896 ---
obs0.1909 20040 99.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.202 Å2
Refinement stepCycle: LAST / Resolution: 1.82→49.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1579 0 19 175 1773
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0221647
X-RAY DIFFRACTIONr_bond_other_d0.0010.021138
X-RAY DIFFRACTIONr_angle_refined_deg1.5421.9712241
X-RAY DIFFRACTIONr_angle_other_deg1.38232770
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4435202
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.18623.10874
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.55715255
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.6061514
X-RAY DIFFRACTIONr_chiral_restr0.0970.2245
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211818
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02327
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.7051.51029
X-RAY DIFFRACTIONr_mcbond_other0.5581.5400
X-RAY DIFFRACTIONr_mcangle_it2.75821678
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.9123618
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.7864.5563
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.822→1.869 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.378 88 -
Rwork0.348 1447 -
obs--100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.5043-0.9166-0.57061.09330.15940.4079-0.10020.13330.171-0.00060.02920.0465-0.0781-0.01260.07090.0963-0.008-0.01790.14790.00540.12822.023-18.707-1.194
20.93550.08480.15240.8262-0.06981.2135-0.03190.00890.01190.07880.01560.0364-0.08260.05910.01630.0403-0.0098-0.00010.078-0.00150.078217.914-21.0058.718
33.52341.51740.85492.50110.9332.2330.046-0.0904-0.16920.0321-0.0966-0.0491-0.0957-0.02340.05060.0233-0.0130.00670.11310.01280.093524.137-24.1682.787
46.27513.724-1.12542.556-0.82980.2884-0.17590.39450.3063-0.11910.22050.30240.013-0.0413-0.04470.2915-0.1155-0.05030.26520.00140.239829.1530.4735.165
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A112 - 141
2X-RAY DIFFRACTION2A142 - 262
3X-RAY DIFFRACTION3A263 - 292
4X-RAY DIFFRACTION4A293 - 318

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