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- PDB-1hr8: Yeast Mitochondrial Processing Peptidase beta-E73Q Mutant Complex... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1hr8 | ||||||
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Title | Yeast Mitochondrial Processing Peptidase beta-E73Q Mutant Complexed with Cytochrome C Oxidase IV Signal Peptide | ||||||
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![]() | HYDROLASE / HxxEH zinc-binding motif | ||||||
Function / homology | ![]() mitochondrial processing peptidase complex / mitochondrial processing peptidase / mitochondrial cytochrome c oxidase assembly / protein processing involved in protein targeting to mitochondrion / Respiratory electron transport / Mitochondrial protein degradation / : / mitochondrial electron transport, cytochrome c to oxygen / endopeptidase activator activity / proton transmembrane transport ...mitochondrial processing peptidase complex / mitochondrial processing peptidase / mitochondrial cytochrome c oxidase assembly / protein processing involved in protein targeting to mitochondrion / Respiratory electron transport / Mitochondrial protein degradation / : / mitochondrial electron transport, cytochrome c to oxygen / endopeptidase activator activity / proton transmembrane transport / mitochondrial intermembrane space / metalloendopeptidase activity / mitochondrial inner membrane / oxidoreductase activity / mitochondrial matrix / mitochondrion / proteolysis / zinc ion binding / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Taylor, A.B. / Smith, B.S. / Kitada, S. / Kojima, K. / Miyaura, H. / Otwinowski, Z. / Ito, A. / Deisenhofer, J. | ||||||
![]() | ![]() Title: Crystal structures of mitochondrial processing peptidase reveal the mode for specific cleavage of import signal sequences. Authors: Taylor, A.B. / Smith, B.S. / Kitada, S. / Kojima, K. / Miyaura, H. / Otwinowski, Z. / Ito, A. / Deisenhofer, J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 630.4 KB | Display | ![]() |
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PDB format | ![]() | 517.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 555.4 KB | Display | ![]() |
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Full document | ![]() | 640.7 KB | Display | |
Data in XML | ![]() | 123.3 KB | Display | |
Data in CIF | ![]() | 165.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1hr6SC ![]() 1hr7C ![]() 1hr9C S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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3 | ![]()
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4 | ![]()
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5 | ![]()
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Unit cell |
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Components
-MITOCHONDRIAL PROCESSING PEPTIDASE ... , 2 types, 8 molecules ACEGBDFH
#1: Protein | Mass: 52532.387 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Plasmid: PTRC99A / Species (production host): Escherichia coli / Production host: ![]() ![]() References: UniProt: P11914, mitochondrial processing peptidase #2: Protein | Mass: 48894.039 Da / Num. of mol.: 4 / Mutation: E73Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Plasmid: PTRC99A / Species (production host): Escherichia coli / Production host: ![]() ![]() References: UniProt: P10507, mitochondrial processing peptidase |
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-Protein/peptide , 1 types, 4 molecules OPQR
#3: Protein/peptide | Mass: 2862.421 Da / Num. of mol.: 4 / Fragment: RESIDUES 2-25 / Source method: obtained synthetically Details: The 24 residue peptide of CYTOCHROME C OXIDASE POLYPEPTIDE IV was synthesized using standard solid-phase Fmoc synthesis methodology References: UniProt: P04037, cytochrome-c oxidase |
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-Non-polymers , 3 types, 10 molecules ![](data/chem/img/EPE.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | #5: Chemical | ChemComp-ZN / #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3 Å3/Da / Density % sol: 59 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | *PLUS Temperature: 21 ℃ / pH: 7.5 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 105 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 2, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.943 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→50 Å / Num. all: 134234 / Num. obs: 134234 / % possible obs: 99.9 % / Redundancy: 6.1 % / Biso Wilson estimate: 47.1 Å2 / Rmerge(I) obs: 0.079 / Net I/σ(I): 23.4 |
Reflection shell | Resolution: 2.7→2.8 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.543 / Mean I/σ(I) obs: 3.5 / % possible all: 100 |
Reflection | *PLUS Num. measured all: 820094 |
Reflection shell | *PLUS % possible obs: 100 % |
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Processing
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Refinement | Starting model: PDB ID 1HR6 Resolution: 2.7→48.63 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 6298765.76 / Data cutoff low absF: 0 / Isotropic thermal model: GROUP / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Maximum Likelihood Function
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 29.8593 Å2 / ksol: 0.323 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 58.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.7→48.63 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: RESTRAINED | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.7→2.8 Å / Rfactor Rfree error: 0.024 / Total num. of bins used: 10
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Xplor file |
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Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS σ(F): 0 / % reflection Rfree: 1.5 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 58.7 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.328 / % reflection Rfree: 1.4 % / Rfactor Rwork: 0.303 |