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Yorodumi- PDB-3lca: Structure of Tom71 complexed with Hsp70 Ssa1 C terminal tail indi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3lca | ||||||
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Title | Structure of Tom71 complexed with Hsp70 Ssa1 C terminal tail indicating conformational plasticity | ||||||
Components |
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Keywords | TRANSPORT PROTEIN / Chaperone / conformational plasticity / Membrane / Mitochondrion / Mitochondrion outer membrane / TPR repeat / Transmembrane | ||||||
Function / homology | Function and homology information : / Regulation of HSF1-mediated heat shock response / mitochondrion targeting sequence binding / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / mitochondria-associated ubiquitin-dependent protein catabolic process / protein insertion into mitochondrial inner membrane / protein import into mitochondrial matrix / fungal-type cell wall / clathrin coat disassembly / response to oxygen levels ...: / Regulation of HSF1-mediated heat shock response / mitochondrion targeting sequence binding / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / mitochondria-associated ubiquitin-dependent protein catabolic process / protein insertion into mitochondrial inner membrane / protein import into mitochondrial matrix / fungal-type cell wall / clathrin coat disassembly / response to oxygen levels / SRP-dependent cotranslational protein targeting to membrane, translocation / protein targeting to mitochondrion / fungal-type vacuole membrane / stress granule disassembly / chaperone cofactor-dependent protein refolding / protein transmembrane transporter activity / protein folding chaperone / heat shock protein binding / transcription repressor complex / ATP-dependent protein folding chaperone / protein polyubiquitination / protein import into nucleus / unfolded protein binding / protein folding / cytoplasmic translation / protein refolding / proteasome-mediated ubiquitin-dependent protein catabolic process / mitochondrial outer membrane / tRNA binding / negative regulation of DNA-templated transcription / ATP hydrolysis activity / mitochondrion / extracellular region / ATP binding / nucleus / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.19 Å | ||||||
Authors | Li, J.Z. / Sha, B.D. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.F / Year: 2010 Title: The structural plasticity of Tom71 for mitochondrial precursor translocations. Authors: Li, J. / Cui, W. / Sha, B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3lca.cif.gz | 113.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3lca.ent.gz | 86.8 KB | Display | PDB format |
PDBx/mmJSON format | 3lca.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lc/3lca ftp://data.pdbj.org/pub/pdb/validation_reports/lc/3lca | HTTPS FTP |
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-Related structure data
Related structure data | 3fp4S 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: 60157.797 Da / Num. of mol.: 1 / Fragment: TPR repeats 1-9, UNP residues 107-639 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P38825 | ||
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#2: Protein/peptide | Mass: 1271.283 Da / Num. of mol.: 1 / Fragment: UNP residues 631-642 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P10591 | ||
#3: Chemical | #4: 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: 2.63 Å3/Da / Density % sol: 53.28 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 20% Ethylene Glycol, 20% PEG 6000, 0.1M Tris, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 200 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.97 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 20, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97 Å / Relative weight: 1 |
Reflection | Resolution: 2.19→50 Å / Num. all: 33761 / Num. obs: 33761 / % possible obs: 98.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5.7 % / Biso Wilson estimate: 40 Å2 / Rmerge(I) obs: 0.095 / Rsym value: 0.095 / Net I/σ(I): 30.8 |
Reflection shell | Resolution: 2.19→2.27 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 2.5 / Num. unique all: 3011 / Rsym value: 0.43 / % possible all: 89.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 3FP4 Resolution: 2.19→8 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.903 / SU B: 11.41 / SU ML: 0.154 / Cross valid method: THROUGHOUT / ESU R: 0.271 / ESU R Free: 0.221 / 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: 34.915 Å2
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Refinement step | Cycle: LAST / Resolution: 2.19→8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.193→2.245 Å / Total num. of bins used: 20
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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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