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- PDB-8gko: Crystal Structure Analysis of Aspergillus fumigatus alkaline protease -
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Open data
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Basic information
Entry | Database: PDB / ID: 8gko | ||||||
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Title | Crystal Structure Analysis of Aspergillus fumigatus alkaline protease | ||||||
![]() | (Alkaline protease ...) x 2 | ||||||
![]() | HYDROLASE / alpha-beta hydrolase | ||||||
Function / homology | ![]() oryzin / symbiont-mediated suppression of host complement activation / elastin catabolic process / fibrinogen binding / IgE binding / serine-type peptidase activity / peptidase activity / serine-type endopeptidase activity / proteolysis / extracellular space / extracellular region Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Fernandez, D. / Diec, D.D.L. / Guo, W. / Russi, S. | ||||||
Funding support | 1items
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![]() | ![]() Title: Targeting Aspergillus allergen oryzin with a chemical probe at atomic precision. Authors: Pattelli, O.N. / Diec, D.D.L. / Guo, W. / Russi, S. / Fernandez, D. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 306.8 KB | Display | ![]() |
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PDB format | ![]() | 247 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 452.5 KB | Display | ![]() |
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Full document | ![]() | 453.7 KB | Display | |
Data in XML | ![]() | 20.4 KB | Display | |
Data in CIF | ![]() | 31.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8gkpC ![]() 8gkqC ![]() 8u45C C: citing same article ( |
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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
-Alkaline protease ... , 2 types, 2 molecules AC
#1: Protein | Mass: 10798.985 Da / Num. of mol.: 1 / Fragment: C-terminal residues 27-121 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Protein | Mass: 28728.674 Da / Num. of mol.: 1 / Fragment: C-terminal residues 122-403 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
-Non-polymers , 5 types, 492 molecules ![](data/chem/img/IMD.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/FOR.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/FOR.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-IMD / | ||||||
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#4: Chemical | ChemComp-EDO / #5: Chemical | #6: Chemical | ChemComp-NA / | #7: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2 Å3/Da / Density % sol: 42.27 % / Description: Rod |
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Crystal grow | Temperature: 289 K / Method: evaporation Details: polyethyleneglycol 550 monomethylether, polyethyleneglycol 20,000, MES/Imidazole buffer |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 17, 2021 Details: Flat Si Rh coated M0, Kirkpatrick-Baez flat bent Si M1 & M2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Liquid nitrogen-cooled double crystal, non fixed exit slit Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97946 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.06→52.577 Å / Num. all: 142896 / Num. obs: 142896 / % possible obs: 93.5 % / Redundancy: 3.8 % / Rpim(I) all: 0.043 / Rrim(I) all: 0.088 / Rsym value: 0.076 / Net I/av σ(I): 6.4 / Net I/σ(I): 8.6 / Num. measured all: 549701 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: ![]() |
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Processing
Software |
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Refinement | Method to determine structure: AB INITIO PHASING / Resolution: 1.06→30.58 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.976 / WRfactor Rfree: 0.1476 / WRfactor Rwork: 0.1276 / FOM work R set: 0.8397 / SU B: 1.096 / SU ML: 0.022 / SU R Cruickshank DPI: 0.0281 / SU Rfree: 0.0281 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.028 / ESU R Free: 0.028 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 71.18 Å2 / Biso mean: 13.191 Å2 / Biso min: 5.7 Å2
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Refinement step | Cycle: final / Resolution: 1.06→30.58 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.06→1.088 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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