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Yorodumi- PDB-4ivg: Crystal structure of mitochondrial Hsp90 (TRAP1) NTD-Middle domai... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4ivg | ||||||
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Title | Crystal structure of mitochondrial Hsp90 (TRAP1) NTD-Middle domain dimer with AMPPNP | ||||||
Components | TNF receptor-associated protein 1 | ||||||
Keywords | CHAPERONE / ATPASE / ATP BINDING / MITOCHONDRIA | ||||||
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 / ATP binding / identical protein binding Similarity search - Function | ||||||
Biological species | Danio rerio (zebrafish) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.749 Å | ||||||
Authors | Partridge, J.R. / Lavery, L.A. / Agard, D.A. | ||||||
Citation | Journal: Mol.Cell / Year: 2014 Title: Structural asymmetry in the closed state of mitochondrial Hsp90 (TRAP1) supports a two-step ATP hydrolysis mechanism. Authors: Lavery, L.A. / Partridge, J.R. / Ramelot, T.A. / Elnatan, D. / 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 | 4ivg.cif.gz | 218.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ivg.ent.gz | 179.3 KB | Display | PDB format |
PDBx/mmJSON format | 4ivg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/iv/4ivg ftp://data.pdbj.org/pub/pdb/validation_reports/iv/4ivg | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 73946.906 Da / Num. of mol.: 1 / Fragment: UNP residues 73-719 / Mutation: G566A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Danio rerio (zebrafish) / Gene: trap1 / Plasmid: PET151/D-TOPO / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-RIL / References: UniProt: A8WFV1 |
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#2: Chemical | ChemComp-ANP / |
#3: Chemical | ChemComp-PO4 / |
#4: Chemical | ChemComp-MG / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.11 Å3/Da / Density % sol: 41.83 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.1M Sodium Phosphate monobasic monohydrate pH 6.5, 12% PEG 8000, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.115869 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 14, 2012 |
Radiation | Monochromator: Double flat crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.115869 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→50 Å / Num. all: 63508 / Num. obs: 63000 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.8 % / Biso Wilson estimate: 29.76 Å2 |
Reflection shell | Resolution: 1.75→1.81 Å / Redundancy: 6.2 % / Mean I/σ(I) obs: 1.44 / % possible all: 94.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.749→29.546 Å / SU ML: 0.2 / σ(F): 1.34 / Phase error: 24.11 / 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: 1.749→29.546 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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