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- PDB-1dxs: Crystal structure of the C-terminal sterile alpha motif (SAM) dom... -

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Basic information

Entry
Database: PDB / ID: 1dxs
TitleCrystal structure of the C-terminal sterile alpha motif (SAM) domain of human p73 alpha splice variant
ComponentsP53-LIKE TRANSCRIPTION FACTOR
KeywordsGENE REGULATION / P73 SAM-LIKE DOMAIN / P53 P63 HOMOLOGUE / STERILE ALPHA MOTIF / TUMOUR SUPRESSOR
Function / homology
Function and homology information


positive regulation of lung ciliated cell differentiation / negative regulation of cardiac muscle cell proliferation / TP53 Regulates Transcription of Death Receptors and Ligands / Activation of PUMA and translocation to mitochondria / Regulation of TP53 Activity through Association with Co-factors / positive regulation of oligodendrocyte differentiation / TP53 regulates transcription of several additional cell death genes whose specific roles in p53-dependent apoptosis remain uncertain / TP53 Regulates Transcription of Caspase Activators and Caspases / TP53 Regulates Transcription of Genes Involved in Cytochrome C Release / negative regulation of neuron differentiation ...positive regulation of lung ciliated cell differentiation / negative regulation of cardiac muscle cell proliferation / TP53 Regulates Transcription of Death Receptors and Ligands / Activation of PUMA and translocation to mitochondria / Regulation of TP53 Activity through Association with Co-factors / positive regulation of oligodendrocyte differentiation / TP53 regulates transcription of several additional cell death genes whose specific roles in p53-dependent apoptosis remain uncertain / TP53 Regulates Transcription of Caspase Activators and Caspases / TP53 Regulates Transcription of Genes Involved in Cytochrome C Release / negative regulation of neuron differentiation / mismatch repair / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / MDM2/MDM4 family protein binding / response to organonitrogen compound / regulation of mitotic cell cycle / transcription corepressor binding / kidney development / protein tetramerization / 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 / RNA polymerase II-specific DNA-binding transcription factor binding / positive regulation of MAPK cascade / transcription cis-regulatory region binding / regulation of cell cycle / DNA-binding transcription factor activity, RNA polymerase II-specific / response to xenobiotic stimulus / cell cycle / positive regulation of apoptotic process / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / negative regulation of cell population proliferation / intracellular membrane-bounded organelle / DNA damage response / chromatin / regulation of transcription by RNA polymerase II / protein kinase binding / positive regulation of DNA-templated transcription / Golgi apparatus / positive regulation of transcription by RNA polymerase II / nucleoplasm / identical protein binding / metal ion binding / nucleus / cytosol
Similarity search - Function
Tumour protein p73, SAM domain / Transcription Factor, Ets-1 / 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 / Transcription Factor, Ets-1 / 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 / DNA polymerase; domain 1 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.54 Å
AuthorsWang, W.K. / Chen, Y.W.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2001
Title: Structure of the C-Terminal Sterile Alpha-Motif (Sam) Domain of Human P73 Alpha
Authors: Wang, W.K. / Bycroft, M. / Foster, N.W. / Buckle, A.M. / Fersht, A.R. / Chen, Y.W.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2000
Title: Crystallization and Preliminary Crystallographic Studies of a Sam Domain at the C-Terminus of Human P73 Alpha
Authors: Wang, W.K. / Proctor, M. / Buckle, A.M. / Bycroft, M. / Chen, Y.W.
#2: Journal: Embo J. / Year: 1999
Title: Solution Structure of a Conserved C-Terminal Domain of P73 with Structural Homology to the Sam Domain
Authors: Chi, S.-W. / Ayed, A. / Arrowsmith, C.H.
History
DepositionJan 15, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 12, 2001Provider: repository / Type: Initial release
Revision 1.1May 7, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 5, 2017Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.4Jan 24, 2018Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name ..._entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain / _entity_src_gen.pdbx_host_org_variant
Revision 1.5Feb 6, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.method / _exptl_crystal_grow.temp
Revision 1.6Dec 6, 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

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Assembly

Deposited unit
A: P53-LIKE TRANSCRIPTION FACTOR


Theoretical massNumber of molelcules
Total (without water)9,0261
Polymers9,0261
Non-polymers00
Water46826
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)32.020, 32.020, 133.840
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-3019-

HOH

21A-3021-

HOH

DetailsBIOLOGICAL_UNIT: MONOMER

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Components

#1: Protein P53-LIKE TRANSCRIPTION FACTOR


Mass: 9026.124 Da / Num. of mol.: 1 / Fragment: C-TERMINAL STERILE ALPHA MOTIF (SAM) DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Cellular location: NUCLEUSCell nucleus / Gene: P73 / Plasmid: MODIFIED PRESET A / Cellular location (production host): CYTOPLASM / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / Variant (production host): C41 / References: UniProt: O15350
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 26 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsRESIDUES GLY-SER (-2 TO -1) CLONING ARTIFACT

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 1.93 Å3/Da / Density % sol: 36 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: CRYSTALLIZED IN 0.1M TRIS-HCL PH8.5, 2.0M MONO-AMMONIUM DIHYDROGEN PHOSPHATE, AT 290K., pH 8.50
Crystal grow
*PLUS
Temperature: 290 K / Method: vapor diffusion, hanging drop
Details: Wang, W.K., (2000) Acta Crystallogr.,Sect.D, 56, 769.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
116 mg/mlprotein1drop
20.1 MTris-HCl1reservoir
32.0 Mammonium dihydrogen orthophosphate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 15, 1999 / Details: MIRRORS
RadiationMonochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.54→26 Å / Num. obs: 2510 / % possible obs: 94.9 % / Observed criterion σ(I): 2 / Redundancy: 6.8 % / Biso Wilson estimate: 59.4 Å2 / Rmerge(I) obs: 0.073 / Rsym value: 0.067 / Net I/σ(I): 7.6
Reflection shellResolution: 2.54→2.71 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.408 / Mean I/σ(I) obs: 2 / Rsym value: 0.377 / % possible all: 97.8

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Processing

Software
NameVersionClassification
CNS0.9refinement
iMOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1COK

1cok


Resolution: 2.54→26 Å / Isotropic thermal model: UNRESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Details: C TERMINAL RESIDUES ARE NOT SEEN IN THE DENSITY MAPS
RfactorNum. reflection% reflectionSelection details
Rfree0.346 269 10.2 %RANDOM
Rwork0.275 ---
obs0.275 2510 94.9 %-
Solvent computationSolvent model: MASKED FLAT MODEL / Bsol: 92.7 Å2 / ksol: 0.352 e/Å3
Displacement parametersBiso mean: 62.1 Å2
Baniso -1Baniso -2Baniso -3
1--9.93 Å20 Å20 Å2
2---9.93 Å20 Å2
3---19.87 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.57 Å0.42 Å
Luzzati d res low-5 Å
Luzzati sigma a0.55 Å0.42 Å
Refinement stepCycle: LAST / Resolution: 2.54→26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms441 0 0 26 467
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d20.4
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.71
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it7.8
X-RAY DIFFRACTIONc_mcangle_it12.1
X-RAY DIFFRACTIONc_scbond_it14
X-RAY DIFFRACTIONc_scangle_it19.4
LS refinement shellResolution: 2.54→2.63 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.483 32 12.9 %
Rwork0.351 207 -
obs--96.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
Software
*PLUS
Name: CNS / Version: 0.9A / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg20.4
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.71

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