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Yorodumi- PDB-6r61: Major aspartyl peptidase 1 from C. neoformans in complex with Inh... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6r61 | ||||||
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Title | Major aspartyl peptidase 1 from C. neoformans in complex with Inhibitor LP258 | ||||||
Components | Endopeptidase | ||||||
Keywords | HYDROLASE / aspartyl protease / secreted / Cryptococcus neoformans / inhibitor complex | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Cryptococcus neoformans (fungus) | ||||||
Method | X-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 1.81 Å | ||||||
Authors | Krystufek, R. / Sacha, P. / Brynda, J. / Konvalinka, J. | ||||||
Funding support | Czech Republic, 1items
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Citation | Journal: To Be Published Title: Major aspartyl peptidase 1 from C. neoformans in complex with Inhibitor LP258 Authors: Krystufek, R. / Sacha, P. / Brynda, J. / Konvalinka, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6r61.cif.gz | 91.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6r61.ent.gz | 65.1 KB | Display | PDB format |
PDBx/mmJSON format | 6r61.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6r61_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 6r61_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 6r61_validation.xml.gz | 17.3 KB | Display | |
Data in CIF | 6r61_validation.cif.gz | 25.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r6/6r61 ftp://data.pdbj.org/pub/pdb/validation_reports/r6/6r61 | HTTPS FTP |
-Related structure data
Related structure data | 6r5hS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
-Protein / Sugars , 2 types, 2 molecules A
#1: Protein | Mass: 36811.281 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: MayI(17-434)-Avitag / Source: (gene. exp.) Cryptococcus neoformans (fungus) / Gene: CNAG_05872 / Plasmid: pMT_BIP_MayI(17-434)Avitag / Production host: Drosophila melanogaster (fruit fly) / Variant (production host): Schneider S2 / References: UniProt: J9VS02 |
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#2: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
-Non-polymers , 7 types, 202 molecules
#3: Chemical | #4: Chemical | ChemComp-PEG / #5: Chemical | ChemComp-SO4 / | #6: Chemical | ChemComp-CL / | #7: Chemical | ChemComp-NA / | #8: Chemical | ChemComp-JT8 / ( | #9: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.41 Å3/Da / Density % sol: 63.96 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop Details: peptidase (85 mg/ml) in 50 mM sodium acetate, pH=5.0, 100mM NaCl in equal volume with reservoir solution: 100mM lithium sulphate, 45% (v/v) PEG-400, 100 mM sodium acetate pH= 4.5 PH range: 4.5 - 5.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 0.9184 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 300K / Detector: PIXEL / Date: Sep 11, 2018 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Confocal Max-Flux optics Rigaku / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9184 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.81→73.78 Å / Num. obs: 44101 / % possible obs: 95.8 % / Redundancy: 3.764 % / Biso Wilson estimate: 24.145 Å2 / CC1/2: 0.991 / Rmerge(I) obs: 0.175 / Rrim(I) all: 0.202 / Χ2: 0.892 / Net I/σ(I): 6.66 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 6R5H Resolution: 1.81→73.78 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.951 / SU B: 2.849 / SU ML: 0.081 / SU R Cruickshank DPI: 0.1073 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.107 / ESU R Free: 0.099 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 115.89 Å2 / Biso mean: 26.587 Å2 / Biso min: 8.6 Å2
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Refinement step | Cycle: final / Resolution: 1.81→73.78 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.81→1.857 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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