+Open data
-Basic information
Entry | Database: PDB / ID: 4d1m | ||||||
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Title | Tetramerization domain of zebrafish p53 (crystal form II) | ||||||
Components | CELLULAR TUMOR ANTIGEN P53P53 | ||||||
Keywords | TRANSCRIPTION / P53 FAMILY / TUMOR SUPPRESSOR / TRANSCRIPTION FACTOR / TETRAMER / PROTEIN EVOLUTION | ||||||
Function / homology | Function and homology information epithelium development / anatomical structure morphogenesis / protein tetramerization / transcription cis-regulatory region binding / cell cycle / DNA-binding transcription factor activity / apoptotic process / identical protein binding / metal ion binding / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | DANIO RERIO (zebrafish) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Joerger, A.C. | ||||||
Citation | Journal: Structure / Year: 2014 Title: Tracing the Evolution of the P53 Tetramerization Domain Authors: Joerger, A.C. / Wilcken, R. / Andreeva, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4d1m.cif.gz | 207.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4d1m.ent.gz | 179.8 KB | Display | PDB format |
PDBx/mmJSON format | 4d1m.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d1/4d1m ftp://data.pdbj.org/pub/pdb/validation_reports/d1/4d1m | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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2 |
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3 |
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Unit cell |
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-Components
#1: Protein/peptide | Mass: 5585.328 Da / Num. of mol.: 12 / Fragment: TETRAMERIZATION DOMAIN, RESIDUES 302-346 Source method: isolated from a genetically manipulated source Source: (gene. exp.) DANIO RERIO (zebrafish) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: G1K2L5 #2: Chemical | #3: Water | ChemComp-HOH / | Sequence details | ADDITIONAL | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.6 Å3/Da / Density % sol: 53 % / Description: NONE |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: SITTING DROP VAPOR DIFFUSION AT 20 DEGREE C; PROTEIN SOLUTION: 12 MG/ML IN 20 MM TRIS PH 7.5, 50 MM NACL, 5 MM DTT; CRYSTALLIZATION BUFFER: 160 MM ZINC ACETATE, 80 MM SODIUM CACODYLATE, PH 6. ...Details: SITTING DROP VAPOR DIFFUSION AT 20 DEGREE C; PROTEIN SOLUTION: 12 MG/ML IN 20 MM TRIS PH 7.5, 50 MM NACL, 5 MM DTT; CRYSTALLIZATION BUFFER: 160 MM ZINC ACETATE, 80 MM SODIUM CACODYLATE, PH 6.5, 12% (W/V) POLYETHYLENE GLYCOL 8,000 AND 19% (W/V) GLYCEROL |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→28.9 Å / Num. obs: 34925 / % possible obs: 99.3 % / Observed criterion σ(I): 2 / Redundancy: 3.4 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 14.8 |
Reflection shell | Resolution: 2.2→2.32 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 2.5 / % possible all: 99.5 |
-Processing
Software | Name: REFMAC / Version: 5.8.0069 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→28.9 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.903 / SU B: 15.086 / SU ML: 0.181 / Cross valid method: THROUGHOUT / ESU R: 0.246 / ESU R Free: 0.219 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 57.722 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→28.9 Å
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