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Open data
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Basic information
Entry | Database: PDB / ID: 6r5h | ||||||
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Title | Major aspartyl peptidase 1 from C. neoformans | ||||||
![]() | Endopeptidase | ||||||
![]() | HYDROLASE / aspartyl protease / secreted / Cryptococcus neoformans | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Krystufek, R. / Sacha, P. / Brynda, J. / Konvalinka, J. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Re-emerging Aspartic Protease Targets: Examining Cryptococcus neoformans Major Aspartyl Peptidase 1 as a Target for Antifungal Drug Discovery. Authors: Krystufek, R. / Sacha, P. / Starkova, J. / Brynda, J. / Hradilek, M. / Tloust'ova, E. / Grzymska, J. / Rut, W. / Boucher, M.J. / Drag, M. / Majer, P. / Hajek, M. / Rezacova, P. / Madhani, H. ...Authors: Krystufek, R. / Sacha, P. / Starkova, J. / Brynda, J. / Hradilek, M. / Tloust'ova, E. / Grzymska, J. / Rut, W. / Boucher, M.J. / Drag, M. / Majer, P. / Hajek, M. / Rezacova, P. / Madhani, H.D. / Craik, C.S. / Konvalinka, 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 | ![]() | 86.5 KB | Display | ![]() |
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PDB format | ![]() | 66.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 807.8 KB | Display | ![]() |
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Full document | ![]() | 810.7 KB | Display | |
Data in XML | ![]() | 17.7 KB | Display | |
Data in CIF | ![]() | 25.7 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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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.) ![]() Strain: H99 / ATCC 208821 / CBS 10515 / FGSC 9487 / Gene: CNAG_05872 / Variant: var. grubii H99 / Plasmid: pMT_BiP_MayI(17-434)CAvi / Production host: ![]() ![]() |
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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 , 9 types, 211 molecules ![](data/chem/img/PGE.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/ACY.gif)
![](data/chem/img/PG4.gif)
![](data/chem/img/1PE.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/ACY.gif)
![](data/chem/img/PG4.gif)
![](data/chem/img/1PE.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-PGE / | ||||||||||||||
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#4: Chemical | ChemComp-PEG / #5: Chemical | ChemComp-EDO / | #6: Chemical | ChemComp-SO4 / #7: Chemical | #8: Chemical | ChemComp-ACY / | #9: Chemical | ChemComp-PG4 / | #10: Chemical | ChemComp-1PE / | #11: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.38 Å3/Da / Density % sol: 63.62 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop Details: MayI(17-434)-Avi (83 mg/mL) in 50 mM sodium acetate, pH 5.0, 100 mM sodium chloride in equal volume with reservoir solution 200 mM lithium sulfate, 45% (v/v) PEG-400, 100 mM NaOAc 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: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 29, 2018 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9184 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.75→48.71 Å / Num. obs: 48515 / % possible obs: 95.8 % / Redundancy: 5.45 % / Biso Wilson estimate: 29.171 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.134 / Rrim(I) all: 0.148 / Χ2: 1.062 / Net I/σ(I): 10.25 / Num. measured all: 264390 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Resolution: 1.75→48.71 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.944 / SU B: 3.025 / SU ML: 0.087 / SU R Cruickshank DPI: 0.0955 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.095 / ESU R Free: 0.096 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: 93.42 Å2 / Biso mean: 29.596 Å2 / Biso min: 15.55 Å2
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Refinement step | Cycle: final / Resolution: 1.75→48.71 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.749→1.795 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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