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Open data
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Basic information
Entry | Database: PDB / ID: 4l3t | ||||||
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Title | Crystal Structure of Substrate-free Human Presequence Protease | ||||||
![]() | (Presequence protease, ...) x 2 | ||||||
![]() | HYDROLASE / zinc metalloendoprotease / mitochondrial matrix | ||||||
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 | ![]() ![]() | ||||||
![]() | King, J.V. / Liang, W.G. / Tang, W.J. | ||||||
![]() | ![]() Title: Molecular basis of substrate recognition and degradation by human presequence protease. Authors: King, J.V. / Liang, W.G. / Scherpelz, K.P. / Schilling, A.B. / Meredith, S.C. / 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 | ![]() | 830.9 KB | Display | ![]() |
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PDB format | ![]() | 702.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 504.8 KB | Display | ![]() |
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Full document | ![]() | 524 KB | Display | |
Data in XML | ![]() | 80.3 KB | Display | |
Data in CIF | ![]() | 113.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related 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: 116454.930 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: 116465.914 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 , 4 types, 1080 molecules ![](data/chem/img/ZN.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | #4: Chemical | ChemComp-GOL / #5: Chemical | ChemComp-ACT / #6: Water | ChemComp-HOH / | |
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-Details
Sequence details | I328V, A397V, AND Q1037R ARE NATURAL VARIANTS. |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.82 Å3/Da / Density % sol: 56.39 % |
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Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 15.2% w/v PEG8000, 15 mM TCEP, 80 mM sodium cacodylate, pH 6.5, 160 mM calcium acetate, 20% v/v glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 291.15K |
-Data collection
Diffraction | Mean temperature: 113.5 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 15, 2012 |
Radiation | Monochromator: Rosenbaum-Rock high-resolution double-crystal Si(111) Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97895 Å / Relative weight: 1 |
Reflection | Resolution: 2.03→50 Å / Num. all: 166830 / Num. obs: 163827 / % possible obs: 98.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.13 % / Biso Wilson estimate: 27.23 Å2 / Rsym value: 0.086 / Net I/σ(I): 17.1 |
Reflection shell | Resolution: 2.03→2.07 Å / Redundancy: 3.8 % / Mean I/σ(I) obs: 2.75 / Num. unique all: 8053 / Rsym value: 0.585 / % possible all: 97 |
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Processing
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Refinement | Method to determine structure: molecular replacement/SAD / Resolution: 2.03→42.547 Å / SU ML: 0.19 / σ(F): 0 / Phase error: 21.36 / Stereochemistry target values: ML Details: THE PRESENCE IN THE ASYMMETRIC UNIT OF TWO PROTEINS WITH DISTINCT PATTERNS OF SIDE CHAIN MODIFICATION REPRESENTS THE BEST FIT TO THE ELECTRON DENSITY AND IS NOT DERIVED FROM THE CO- ...Details: THE PRESENCE IN THE ASYMMETRIC UNIT OF TWO PROTEINS WITH DISTINCT PATTERNS OF SIDE CHAIN MODIFICATION REPRESENTS THE BEST FIT TO THE ELECTRON DENSITY AND IS NOT DERIVED FROM THE CO-CRYSTALLIZATION OF TWO CHEMICALLY DISTINCT PROTEINS.
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Solvent computation | Shrinkage radii: 0.6 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 53.486 Å2 / ksol: 0.38 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 36.11 Å2
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Refinement step | Cycle: LAST / Resolution: 2.03→42.547 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: 84.7848 Å / Origin y: 56.4114 Å / Origin z: -38.4891 Å
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Refinement TLS group | Selection details: all |