+Open data
-Basic information
Entry | Database: PDB / ID: 4d1l | ||||||
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Title | Tetramerization domain of zebrafish p53 (crystal form I) | ||||||
Components | CELLULAR TUMOR ANTIGEN P53 | ||||||
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 / DNA-binding transcription factor activity / apoptotic process / identical protein binding / nucleus / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | DANIO RERIO (zebrafish) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.97 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 | 4d1l.cif.gz | 111 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4d1l.ent.gz | 88.1 KB | Display | PDB format |
PDBx/mmJSON format | 4d1l.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4d1l_validation.pdf.gz | 470 KB | Display | wwPDB validaton report |
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Full document | 4d1l_full_validation.pdf.gz | 471.1 KB | Display | |
Data in XML | 4d1l_validation.xml.gz | 10.6 KB | Display | |
Data in CIF | 4d1l_validation.cif.gz | 14.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d1/4d1l ftp://data.pdbj.org/pub/pdb/validation_reports/d1/4d1l | HTTPS FTP |
-Related structure data
Related structure data | 4cz5C 4cz6C 4cz7C 4d1mC 1c26S C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein/peptide | Mass: 5585.328 Da / Num. of mol.: 6 / 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: 2.4 Å3/Da / Density % sol: 49 % / 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: 50 MM ZINC ACETATE AND 20% (W/V) POLYETHYLENE GLYCOL 3,350. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 |
Detector | Type: ADSC CCD / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 |
Reflection | Resolution: 1.97→28.5 Å / Num. obs: 23226 / % possible obs: 99.6 % / Observed criterion σ(I): 2 / Redundancy: 5.5 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 18.1 |
Reflection shell | Resolution: 1.97→2.08 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.65 / Mean I/σ(I) obs: 2.8 / % possible all: 99.3 |
-Processing
Software | Name: REFMAC / Version: 5.8.0071 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1C26 Resolution: 1.97→28.5 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.942 / SU B: 8.44 / SU ML: 0.119 / Cross valid method: THROUGHOUT / ESU R: 0.164 / ESU R Free: 0.149 / 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: 55.187 Å2
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Refinement step | Cycle: LAST / Resolution: 1.97→28.5 Å
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Refine LS restraints |
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