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Yorodumi- PDB-2ciu: Structure of the IMS domain of the mitochondrial import protein T... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2ciu | ||||||
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Title | Structure of the IMS domain of the mitochondrial import protein Tim21 from S. cerevisiae | ||||||
Components | IMPORT INNER MEMBRANE TRANSLOCASE SUBUNIT TIM21 MITOCHONDRIAL | ||||||
Keywords | PROTEIN TRANSPORT / MITOCHONDRIAL IMPORT / INNER MEMBRANE / MEMBRANE / MITOCHONDRION / TRANSIT PEPTIDE / TRANSLOCATION / TRANSMEMBRANE / TRANSPORT | ||||||
Function / homology | Function and homology information TIM23 mitochondrial import inner membrane translocase complex / protein import into mitochondrial matrix / protein insertion into mitochondrial inner membrane / mitochondrial inner membrane / mitochondrion Similarity search - Function | ||||||
Biological species | SACCHAROMYCES CEREVISIAE (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.6 Å | ||||||
Authors | Albrecht, R. / Zeth, K. / Rehling, P. / Pfanner, N. | ||||||
Citation | Journal: Embo Rep. / Year: 2006 Title: The Tim21 Binding Domain Connects the Preprotein Translocases of Both Mitochondrial Membranes Authors: Albrecht, R. / Rehling, P. / Chacinska, A. / Brix, J. / Cadamuro, S.A. / Volkmer, R. / Guiard, B. / Pfanner, N. / Zeth, K. | ||||||
History |
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Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2ciu.cif.gz | 41.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2ciu.ent.gz | 28.4 KB | Display | PDB format |
PDBx/mmJSON format | 2ciu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2ciu_validation.pdf.gz | 420.1 KB | Display | wwPDB validaton report |
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Full document | 2ciu_full_validation.pdf.gz | 420.7 KB | Display | |
Data in XML | 2ciu_validation.xml.gz | 8.7 KB | Display | |
Data in CIF | 2ciu_validation.cif.gz | 12 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ci/2ciu ftp://data.pdbj.org/pub/pdb/validation_reports/ci/2ciu | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 14763.003 Da / Num. of mol.: 1 / Fragment: IMS DOMAIN, RESIDUES 103-225 Source method: isolated from a genetically manipulated source Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast) Organ: MITOCHONDRIUM / Plasmid: PPROEXHTA / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P53220 |
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#2: Water | ChemComp-HOH / |
Compound details | ESSENTIAL COMPONENT OF THE TIM23 COMPLEX, A COMPLEX THAT MEDIATES THE TRANSLOCATION OF TRANSIT ...ESSENTIAL COMPONENT OF THE TIM23 COMPLEX, A COMPLEX THAT MEDIATES THE TRANSLOCAT |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.02 Å3/Da / Density % sol: 39 % |
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Crystal grow | pH: 6 / Details: 0.2 M LI2SO4, 0.1 M BIS-TRIS PH 6.5, 25% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 1.05 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jan 29, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.05 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→20 Å / Num. obs: 16515 / % possible obs: 97.5 % / Observed criterion σ(I): 3.72 / Redundancy: 3.33 % / Biso Wilson estimate: 21.4 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 18 |
Reflection shell | Resolution: 1.58→1.68 Å / Redundancy: 3.27 % / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 3.72 / % possible all: 94 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.6→20 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 909332.09 / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Bsol: 68.9141 Å2 / ksol: 0.419383 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.9 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.6→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.6→1.7 Å / Rfactor Rfree error: 0.025 / Total num. of bins used: 6
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Xplor file |
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