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- PDB-4rpu: Crystal Structure of Human Presequence Protease in Complex with I... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4rpu | ||||||
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Title | Crystal Structure of Human Presequence Protease in Complex with Inhibitor MitoBloCK-60 | ||||||
![]() | (Presequence protease, ...) x 2 | ||||||
![]() | hydrolase/hydrolase inhibitor / hydrolase-hydrolase inhibitor complex | ||||||
Function / homology | ![]() Mitochondrial protein import / protein targeting to mitochondrion / Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases / enzyme activator activity / protein processing / metalloendopeptidase activity / metallopeptidase activity / mitochondrial matrix / mitochondrion / proteolysis / zinc ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Mo, S.M. / Liang, W.G. / King, J.V. / Wijaya, J. / Koehler, C.M. / Tang, W.J. | ||||||
![]() | ![]() Title: Crystal Structure of Human Presequence Protease in Complex with Inhibitor MitoBloCK-60 Authors: Mo, S.M. / Liang, W.G. / King, J.V. / Wijaya, J. / Koehler, C.M. / Tang, W.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 | ![]() | 826.7 KB | Display | ![]() |
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PDB format | ![]() | 701.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.6 MB | Display | ![]() |
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Full document | ![]() | 1.6 MB | Display | |
Data in XML | ![]() | 80.8 KB | Display | |
Data in CIF | ![]() | 111.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
-Presequence protease, ... , 2 types, 2 molecules AB
#1: Protein | Mass: 115823.789 Da / Num. of mol.: 1 / Fragment: UNP residues 33-1037 / Mutation: E107Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q5JRX3, Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases |
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#2: Protein | Mass: 115793.695 Da / Num. of mol.: 1 / Fragment: UNP residues 33-1037 / Mutation: E107Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q5JRX3, Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases |
-Non-polymers , 6 types, 845 molecules ![](data/chem/img/ZN.gif)
![](data/chem/img/3UE.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/3UE.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | #4: Chemical | ChemComp-3UE / [ #5: Chemical | ChemComp-GOL / #6: Chemical | ChemComp-ACT / #7: Chemical | #8: Water | ChemComp-HOH / | |
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-Details
Sequence details | THE CONFLICTS ARE DUE TO GENETIC VARIATION |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.84 Å3/Da / Density % sol: 56.75 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.7 Details: 15.0% PEG 8000, 15 mM TCEP, 80 mM sodium cacodylate pH 6.7, 160 mM calcium acetate, 20% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 2.27→50 Å / Num. all: 120522 / Num. obs: 119317 / % possible obs: 99 % / Observed criterion σ(F): 2.1 / Observed criterion σ(I): 2.1 |
Reflection shell | Resolution: 2.27→2.31 Å / Redundancy: 3.3 % / Mean I/σ(I) obs: 2.1 / Rsym value: 0.675 / % possible all: 98 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.265→44.853 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 36.4444 Å / Origin y: 53.5367 Å / Origin z: 24.4747 Å
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Refinement TLS group | Selection details: all |