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Yorodumi- PDB-3ebm: Crystal structure of human translationally controlled tumour asso... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3ebm | ||||||
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Title | Crystal structure of human translationally controlled tumour associated protein (hTCTP) mutant E12V | ||||||
Components | Translationally-controlled tumor protein | ||||||
Keywords | CALCIUM-BINDING PROTEIN / TCTP / E12V / Calcium / Cytoplasm / Phosphoprotein | ||||||
Function / homology | Function and homology information negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage / cytoplasmic microtubule / multivesicular body / response to virus / spindle pole / intracellular calcium ion homeostasis / calcium ion transport / regulation of apoptotic process / calcium ion binding / negative regulation of apoptotic process ...negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage / cytoplasmic microtubule / multivesicular body / response to virus / spindle pole / intracellular calcium ion homeostasis / calcium ion transport / regulation of apoptotic process / calcium ion binding / negative regulation of apoptotic process / extracellular space / RNA binding / extracellular exosome / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||
Authors | Yang, B. / Dong, X. / Zhong, C. / Ding, J. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2009 Title: Molecular basis of the acceleration of the GDP-GTP exchange of human ras homolog enriched in brain by human translationally controlled tumor protein. Authors: Dong, X. / Yang, B. / Li, Y. / Zhong, C. / Ding, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3ebm.cif.gz | 234 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ebm.ent.gz | 189.3 KB | Display | PDB format |
PDBx/mmJSON format | 3ebm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/eb/3ebm ftp://data.pdbj.org/pub/pdb/validation_reports/eb/3ebm | HTTPS FTP |
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-Related structure data
Related structure data | 1yz1S S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 20660.516 Da / Num. of mol.: 4 / Mutation: E12V Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TPT1 / Plasmid: pET-22b+ / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P13693 #2: Water | ChemComp-HOH / | |
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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: 2.7 Å3/Da / Density % sol: 54.42 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.2 Details: 0.1M Tris, pH 8.2, 22% PEG 6000, VAPOR DIFFUSION, HANGING DROP, temperature 277.0K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: May 25, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→50 Å / Num. all: 28188 / Num. obs: 27483 / % possible obs: 97.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4 % / Rmerge(I) obs: 0.096 / Rsym value: 0.096 / Net I/σ(I): 13.6 |
Reflection shell | Resolution: 2.6→2.69 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.467 / Mean I/σ(I) obs: 2.9 / Rsym value: 0.467 / % possible all: 97.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1YZ1 Resolution: 2.6→36 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.907 / SU B: 28.599 / SU ML: 0.267 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.322 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: 55.88 Å2
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Refinement step | Cycle: LAST / Resolution: 2.6→36 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.602→2.669 Å / Total num. of bins used: 20
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