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- PDB-7y1x: Crystal structure of prolyl oligopeptidase from Microbulbifer are... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7y1x | ||||||
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Title | Crystal structure of prolyl oligopeptidase from Microbulbifer arenaceous complex with PEG400 and MES | ||||||
![]() | prolyl oligopeptidase | ||||||
![]() | HYDROLASE / S9A / prolyl endopeptidase / serine protease / mental disorder / amnesia | ||||||
Function / homology | DI(HYDROXYETHYL)ETHER![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Huang, P. / Jiang, Z.Q. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Crystal structure of prolyl oligopeptidase from Microbulbifer arenaceous complex with PEG400 and MES Authors: Huang, P. / Jiang, Z.Q. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 167.9 KB | Display | ![]() |
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PDB format | ![]() | 124.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3munS 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 A
#1: Protein | Mass: 79952.180 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Non-polymers , 5 types, 531 molecules ![](data/chem/img/1PE.gif)
![](data/chem/img/MES.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MES.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | ChemComp-MES / #4: Chemical | ChemComp-PEG / | #5: Chemical | ChemComp-SO4 / | #6: 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: 2.19 Å3/Da / Density % sol: 43.88 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 0.04 M MES monohydrate pH 6.0, 8.8% (v/v) polyethylene glycol 400 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 S 2M / Detector: PIXEL / Date: Jun 27, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97944 Å / Relative weight: 1 |
Reflection | Resolution: 1.67→50 Å / Num. obs: 75931 / % possible obs: 94.38 % / Redundancy: 6.7 % / CC1/2: 0.998 / Net I/σ(I): 15.11 |
Reflection shell | Resolution: 1.67→1.7 Å / Num. unique obs: 7149 / CC1/2: 0.899 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3MUN Resolution: 1.67→31.651 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.951 / SU B: 1.705 / SU ML: 0.057 / Cross valid method: THROUGHOUT / ESU R: 0.099 / ESU R Free: 0.095 / Details: Hydrogens have not been used
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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: BABINET MODEL PLUS MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.037 Å2
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Refinement step | Cycle: LAST / Resolution: 1.67→31.651 Å
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Refine LS restraints |
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LS refinement shell |
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