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Open data
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Basic information
Entry | Database: PDB / ID: 7z6t | ||||||
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Title | Aspergillus clavatus M36 protease without the propeptide | ||||||
![]() | Extracellular metalloproteinase mep | ||||||
![]() | PEPTIDE BINDING PROTEIN / Keratinase / Protease / Metalloprotein / RECOMBINATION | ||||||
Function / homology | ![]() Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases / metalloendopeptidase activity / proteolysis / extracellular space / zinc ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Wilkens, C. / Qiu, J. / Meyer, A.S. / Morth, J.P. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Aspergillus clavatus M36 protease without the propeptide Authors: Wilkens, C. / Qiu, J. / Meyer, A.S. / Morth, J.P. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 114.1 KB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 7 MB | Display | ![]() |
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Full document | ![]() | 7 MB | Display | |
Data in XML | ![]() | 23 KB | Display | |
Data in CIF | ![]() | 34.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4k90S S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-Protein , 1 types, 1 molecules AAA
#1: Protein | Mass: 42573.039 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: ATCC 1007 / CBS 513.65 / DSM 816 / NCTC 3887 / NRRL 1 / QM 1276 / 107 Gene: mep, ACLA_060300 / Production host: ![]() References: UniProt: A1C4M2, Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases |
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-Sugars , 2 types, 2 molecules
#2: Polysaccharide | alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-[alpha-D-mannopyranose-(1-6)]alpha-D- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Type: oligosaccharide / Mass: 1235.105 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source |
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#3: Polysaccharide | beta-D-mannopyranose-(1-3)-D-mannose Type: oligosaccharide / Mass: 342.297 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source |
-Non-polymers , 6 types, 470 molecules ![](data/chem/img/EDO.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | ChemComp-EDO / #5: Chemical | ChemComp-ZN / | #6: Chemical | ChemComp-CA / | #7: Chemical | ChemComp-SO4 / #8: Chemical | ChemComp-NA / | #9: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.77 Å3/Da / Density % sol: 55.61 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.1 M HEPES pH 7.5, 0.2 M lithium sulfate, 25% PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 24, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9762 Å / Relative weight: 1 |
Reflection | Resolution: 1.51→45.04 Å / Num. obs: 71273 / % possible obs: 98.72 % / Redundancy: 6.3 % / CC1/2: 0.8 / Net I/σ(I): 12.25 |
Reflection shell | Resolution: 1.51→1.564 Å / Num. unique obs: 6523 / CC1/2: 0.2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4k90 Resolution: 1.51→45.04 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.953 / SU B: 1.771 / SU ML: 0.063 / Cross valid method: FREE R-VALUE / ESU R: 0.073 / ESU R Free: 0.071 Details: Hydrogens have been used if present in the input file
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.884 Å2
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Refinement step | Cycle: LAST / Resolution: 1.51→45.04 Å
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Refine LS restraints |
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LS refinement shell |
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