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Yorodumi- PDB-5tvu: Crystal structure of mitochondrial Hsp90 (TRAP1) with ATP in abse... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5tvu | ||||||
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Title | Crystal structure of mitochondrial Hsp90 (TRAP1) with ATP in absence of Mg | ||||||
Components | TNF receptor-associated protein 1 | ||||||
Keywords | CHAPERONE / Hsp90 / ATP / TRAP1 / Structural Genomics / PSI-2 / Protein Structure Initiative | ||||||
Function / homology | Function and homology information : / nucleic acid metabolic process / ATP-dependent protein folding chaperone / unfolded protein binding / protein folding / mitochondrial inner membrane / calcium ion binding / protein kinase binding / magnesium ion binding / ATP hydrolysis activity ...: / nucleic acid metabolic process / ATP-dependent protein folding chaperone / unfolded protein binding / protein folding / mitochondrial inner membrane / calcium ion binding / protein kinase binding / magnesium ion binding / ATP hydrolysis activity / ATP binding / identical protein binding Similarity search - Function | ||||||
Biological species | Danio rerio (zebrafish) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å | ||||||
Authors | Elnatan, D. / Betegon, M. / Agard, D.A. | ||||||
Funding support | United States, 1items
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Citation | Journal: Elife / Year: 2017 Title: Symmetry broken and rebroken during the ATP hydrolysis cycle of the mitochondrial Hsp90 TRAP1. Authors: Elnatan, D. / Betegon, M. / Liu, Y. / Ramelot, T. / Kennedy, M.A. / Agard, D.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5tvu.cif.gz | 496.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5tvu.ent.gz | 406.3 KB | Display | PDB format |
PDBx/mmJSON format | 5tvu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5tvu_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 5tvu_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 5tvu_validation.xml.gz | 24.7 KB | Display | |
Data in CIF | 5tvu_validation.cif.gz | 36 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tv/5tvu ftp://data.pdbj.org/pub/pdb/validation_reports/tv/5tvu | HTTPS FTP |
-Related structure data
Related structure data | 5tthC 5tvwC 5tvxC 4ipeS 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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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 74635.625 Da / Num. of mol.: 2 / Fragment: UNP residues 73-719 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Danio rerio (zebrafish) / Gene: trap1 / Variant: delta1-72 / Plasmid: pET151DTOPO / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)-RIL / References: UniProt: A8WFV1, UniProt: F1Q9X9*PLUS #2: Chemical | |
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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: 2.31 Å3/Da / Density % sol: 46.72 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop Details: 0.2 M NaK Tartrate, 20% (v/v) PEG3350, 36 mM hexamine cobalt, 5 mM ATP,5 mM EDTA |
-Data collection
Diffraction | Mean temperature: 91.4 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.1159 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 1, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1159 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→44.52 Å / Num. obs: 61835 / % possible obs: 93.4 % / Redundancy: 1.8 % / CC1/2: 0.734 / Net I/σ(I): 2.2 |
Reflection shell | Resolution: 2.3→2.39 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4IPE Resolution: 3.5→39.759 Å / SU ML: 0.44 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.47 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.5→39.759 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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