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Yorodumi- PDB-1yz1: Crystal structure of human translationally controlled tumour asso... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1yz1 | ||||||
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Title | Crystal structure of human translationally controlled tumour associated protein | ||||||
Components | Translationally controlled tumor protein | ||||||
Keywords | UNKNOWN FUNCTION / tumor protein | ||||||
Function / homology | Function and homology information negative regulation of ectoderm development / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage / stem cell population maintenance / cytoplasmic microtubule / multivesicular body / response to virus / intracellular calcium ion homeostasis / spindle pole / calcium ion transport / regulation of apoptotic process ...negative regulation of ectoderm development / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage / stem cell population maintenance / cytoplasmic microtubule / multivesicular body / response to virus / intracellular calcium ion homeostasis / spindle pole / calcium ion transport / regulation of apoptotic process / DNA-binding transcription factor binding / calcium ion binding / negative regulation of apoptotic process / extracellular space / RNA binding / extracellular exosome / nucleoplasm / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Cavarelli, J. / Moras, D. / Amson, R. / Telerman, A. | ||||||
Citation | Journal: Cell Death Differ. / Year: 2008 Title: TCTP protects from apoptotic cell death by antagonizing bax function Authors: Susini, L. / Besse, S. / Duflaut, D. / Lespagnol, A. / Beekman, C. / Fiucci, G. / Atkinson, A.R. / Busso, D. / Poussin, P. / Marine, J.C. / Martinou, J.C. / Cavarelli, J. / Moras, D. / Amson, R. / Telerman, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1yz1.cif.gz | 139.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1yz1.ent.gz | 109.1 KB | Display | PDB format |
PDBx/mmJSON format | 1yz1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yz/1yz1 ftp://data.pdbj.org/pub/pdb/validation_reports/yz/1yz1 | HTTPS FTP |
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-Related structure data
Related structure data | 1h7yS 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: 19895.633 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / 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: 2.3 Å3/Da / Density % sol: 47.3 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion / pH: 6.2 Details: PEG 5000, pH 6.2, VAPOR DIFFUSION, temperature 277K |
-Data collection
Diffraction | Mean temperature: 140 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: May 15, 2004 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.934 Å / Relative weight: 1 |
Reflection | Resolution: 1.94→50 Å / Num. all: 55405 / Num. obs: 54464 / % possible obs: 98.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.8 % / Biso Wilson estimate: 21.8 Å2 / Rsym value: 0.04 |
Reflection shell | Resolution: 1.94→1.99 Å / Redundancy: 2.6 % / Num. unique all: 3667 / Rsym value: 0.154 / % possible all: 98.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1H7Y Resolution: 2→25 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 77.0166 Å2 / ksol: 0.454136 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.3 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2→25 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.13 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 6
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Xplor file |
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