+Open data
-Basic information
Entry | Database: PDB / ID: 2cw9 | ||||||
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Title | Crystal structure of human Tim44 C-terminal domain | ||||||
Components | translocase of inner mitochondrial membrane | ||||||
Keywords | PROTEIN TRANSPORT / Structure Genomics / TIM / Structural Genomics / NPPFSA / RIKEN Structural Genomics/Proteomics Initiative / RSGI / NPPSFA / National Project on Protein Structural and Functional Analyses | ||||||
Function / homology | Function and homology information protein import into mitochondrial matrix / Mitochondrial protein import / protein targeting to mitochondrion / protein-folding chaperone binding / mitochondrial inner membrane / mitochondrial matrix / mitochondrion / ATP binding Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å | ||||||
Authors | Handa, N. / Kishishita, S. / Morita, S. / Kinoshita, Y. / Nagano, Y. / Uda, H. / Terada, T. / Uchikubo, T. / Takemoto, C. / Jin, Z. ...Handa, N. / Kishishita, S. / Morita, S. / Kinoshita, Y. / Nagano, Y. / Uda, H. / Terada, T. / Uchikubo, T. / Takemoto, C. / Jin, Z. / Chrzas, J. / Chen, L. / Liu, Z.-J. / Wang, B.-C. / Shirouzu, M. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2007 Title: Structure of the human Tim44 C-terminal domain in complex with pentaethylene glycol: ligand-bound form. Authors: Handa, N. / Kishishita, S. / Morita, S. / Akasaka, R. / Jin, Z. / Chrzas, J. / Chen, L. / Liu, Z.J. / Wang, B.C. / Sugano, S. / Tanaka, A. / Terada, T. / Shirouzu, M. / Yokoyama, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2cw9.cif.gz | 49.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2cw9.ent.gz | 38.9 KB | Display | PDB format |
PDBx/mmJSON format | 2cw9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2cw9_validation.pdf.gz | 436.6 KB | Display | wwPDB validaton report |
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Full document | 2cw9_full_validation.pdf.gz | 437.9 KB | Display | |
Data in XML | 2cw9_validation.xml.gz | 10.7 KB | Display | |
Data in CIF | 2cw9_validation.cif.gz | 14.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cw/2cw9 ftp://data.pdbj.org/pub/pdb/validation_reports/cw/2cw9 | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 21935.025 Da / Num. of mol.: 1 / Fragment: C-TERMINAL DOMAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Description: Cell free / References: UniProt: O43615 | ||
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#2: Chemical | #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: 4.2 Å3/Da / Density % sol: 70.6 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: PEG400, HEPES, ammonium sulfate, glycerol, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.9792 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: May 23, 2005 / Details: mirrors |
Radiation | Monochromator: Si / Protocol: SAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→50 Å / Num. obs: 31350 / % possible obs: 99.1 % / Observed criterion σ(I): 0 / Redundancy: 8.2 % / Biso Wilson estimate: 20.5 Å2 / Rsym value: 0.065 / Net I/σ(I): 25.6 |
Reflection shell | Resolution: 1.9→1.97 Å / Mean I/σ(I) obs: 3.9 / Rsym value: 0.313 / % possible all: 95.7 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.9→19.93 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 2021435.15 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 58.4 Å2 / ksol: 0.364381 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 34.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.9→19.93 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→2.02 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
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Xplor file |
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