+Open data
-Basic information
Entry | Database: PDB / ID: 3qk9 | ||||||
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Title | Yeast Tim44 C-terminal domain complexed with Cymal-3 | ||||||
Components | Mitochondrial import inner membrane translocase subunit TIM44 | ||||||
Keywords | PROTEIN TRANSPORT / Mitochondrion | ||||||
Function / homology | Function and homology information PAM complex, Tim23 associated import motor / extrinsic component of mitochondrial inner membrane / TIM23 mitochondrial import inner membrane translocase complex / protein import into mitochondrial matrix / intracellular protein transport / protein-macromolecule adaptor activity / protein-folding chaperone binding / mitochondrial inner membrane / mitochondrion / ATP binding Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å | ||||||
Authors | Cui, W. / Josyula, R. / Fu, Z. / Sha, B. | ||||||
Citation | Journal: Protein Pept.Lett. / Year: 2011 Title: Membrane Binding Mechanism of Yeast Mitochondrial Peripheral Membrane Protein TIM44. Authors: Cui, W. / Josyula, R. / Li, J. / Fu, Z. / Sha, B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3qk9.cif.gz | 151 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3qk9.ent.gz | 122.1 KB | Display | PDB format |
PDBx/mmJSON format | 3qk9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qk/3qk9 ftp://data.pdbj.org/pub/pdb/validation_reports/qk/3qk9 | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 25440.000 Da / Num. of mol.: 2 / Fragment: Residues 210-431 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: TIM44, ISP45, MIM44, MPI1, YIL022W / Production host: Escherichia coli (E. coli) / References: UniProt: Q01852 #2: Chemical | #3: 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: 3.01 Å3/Da / Density % sol: 59.15 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 1.0M Ammonium Sulfate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-BM-B / Wavelength: 0.998 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Oct 19, 2008 |
Radiation | Monochromator: insertion device / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.998 Å / Relative weight: 1 |
Reflection | Resolution: 3.1→40 Å / Num. all: 11326 / Num. obs: 11326 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.1→32.93 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.877 / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / ESU R Free: 5.056 / 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: 106.923 Å2
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Refinement step | Cycle: LAST / Resolution: 3.1→32.93 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.1→3.179 Å / Total num. of bins used: 20
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