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Yorodumi- PDB-3dxr: Crystal structure of the yeast inter-membrane space chaperone ass... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3dxr | ||||||
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Title | Crystal structure of the yeast inter-membrane space chaperone assembly TIM9.10 | ||||||
Components |
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Keywords | PROTEIN TRANSPORT / Alpha-Propeller / Helix-Turn-Helix / Intramolecular Disulfides. / Chaperone / Inner membrane / Membrane / Metal-binding / Mitochondrion / Translocation / Transport / Zinc | ||||||
Function / homology | Function and homology information mitochondrial intermembrane space protein transporter complex / Mitochondrial protein import / TIM22 mitochondrial import inner membrane insertion complex / protein transporter activity / protein insertion into mitochondrial inner membrane / mitochondrial intermembrane space / unfolded protein binding / mitochondrial inner membrane / mitochondrion / metal ion binding Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.5 Å | ||||||
Authors | Webb, C.T. / Gulbis, J.M. | ||||||
Citation | Journal: Mol Biol Cell / Year: 2009 Title: Structural and functional requirements for activity of the Tim9-Tim10 complex in mitochondrial protein import Authors: Baker, M.J. / Webb, C.T. / Stroud, D.A. / Palmer, C.S. / Frazier, A.E. / Guiard, B. / Chacinska, A. / Gulbis, J.M. / Ryan, M.T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3dxr.cif.gz | 41.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3dxr.ent.gz | 28 KB | Display | PDB format |
PDBx/mmJSON format | 3dxr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3dxr_validation.pdf.gz | 442.8 KB | Display | wwPDB validaton report |
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Full document | 3dxr_full_validation.pdf.gz | 445.6 KB | Display | |
Data in XML | 3dxr_validation.xml.gz | 8.2 KB | Display | |
Data in CIF | 3dxr_validation.cif.gz | 10.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dx/3dxr ftp://data.pdbj.org/pub/pdb/validation_reports/dx/3dxr | HTTPS FTP |
-Related structure data
Related structure data | 2bskS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 10360.779 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: TIM9 / Plasmid: PGEX-4T2 / Production host: Escherichia coli (E. coli) / Strain (production host): Origami DE3 pLysS / References: UniProt: O74700 |
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#2: Protein | Mass: 10457.718 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: MRS11, TIM10 / Plasmid: PGEX-4T2 / Production host: Escherichia coli (E. coli) / Strain (production host): Origami DE3 pLysS / References: UniProt: P87108 |
#3: 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: 1.93 Å3/Da / Density % sol: 36.42 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 100 mM MES, 3M Na Formate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9762 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 12, 2006 / Details: Single Silicon (111) monochromator | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Silicon (111) crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9762 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Redundancy: 7 % / Av σ(I) over netI: 19.8 / Number: 40039 / Rmerge(I) obs: 0.087 / Χ2: 1.02 / D res high: 2.5 Å / D res low: 50 Å / Num. obs: 5723 / % possible obs: 97.8 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Diffraction reflection shell |
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Reflection | Resolution: 2.5→50 Å / Num. all: 5852 / Num. obs: 5723 / % possible obs: 97.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7 % / Rmerge(I) obs: 0.087 / Χ2: 1.022 / Net I/σ(I): 19.8 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Resolution: 2.5→2.59 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 5.47 / Num. unique all: 570 / Rsym value: 0.4 / Χ2: 0.977 / % possible all: 99.7 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 2BSK Resolution: 2.5→50 Å / Occupancy max: 1 / Occupancy min: 1 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber / Details: Maximum likelihood refinement in CNS
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Solvent computation | Bsol: 92.938 Å2 | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 153.34 Å2 / Biso mean: 78.151 Å2 / Biso min: 35.34 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.5→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.61 Å / Rfactor Rfree error: 0.001
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Xplor file |
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