[English] 日本語
Yorodumi- PDB-7vgb: Crystal structure of apo prolyl oligopeptidase from Microbulbifer... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7vgb | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of apo prolyl oligopeptidase from Microbulbifer arenaceous | ||||||
Components | prolyl oligopeptidaseProlyl endopeptidase | ||||||
Keywords | HYDROLASE / S9A / prolyl endopeptidase / serine protease / mental disorder / amnesia | ||||||
Function / homology | IMIDAZOLE / NICKEL (II) ION / DI(HYDROXYETHYL)ETHER / trimethylamine oxide Function and homology information | ||||||
Biological species | Microbulbifer arenaceous (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.227 Å | ||||||
Authors | Huang, P. / Jiang, Z.Q. | ||||||
Funding support | China, 1items
| ||||||
Citation | Journal: Acta Crystallogr D Struct Biol / Year: 2022 Title: The structure and molecular dynamics of prolyl oligopeptidase from Microbulbifer arenaceous provide insights into catalytic and regulatory mechanisms. Authors: Huang, P. / Lv, A. / Yan, Q. / Jiang, Z. / Yang, S. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 7vgb.cif.gz | 313.4 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb7vgb.ent.gz | 240 KB | Display | PDB format |
PDBx/mmJSON format | 7vgb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vg/7vgb ftp://data.pdbj.org/pub/pdb/validation_reports/vg/7vgb | HTTPS FTP |
---|
-Related structure data
Related structure data | 7vgcC 3munS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 79952.180 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Microbulbifer arenaceous (bacteria) Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: prolyl oligopeptidase |
---|
-Non-polymers , 7 types, 1034 molecules
#2: Chemical | ChemComp-GOL / #3: Chemical | ChemComp-IMD / | #4: Chemical | ChemComp-TRS / #5: Chemical | #6: Chemical | #7: Chemical | #8: Water | ChemComp-HOH / | |
---|
-Details
Has ligand of interest | Y |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.19 Å3/Da / Density % sol: 43.96 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.2M Trimethylamine N-oxide dihydrate, 0.1M Tris pH 8.5, 20% (w/v) Polyethylene glycol monomethyl ether 2000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.979 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 8, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.227→44.198 Å / Num. obs: 64538 / % possible obs: 99.86 % / Redundancy: 6.8 % / Biso Wilson estimate: 19.9 Å2 / CC1/2: 0.994 / CC star: 0.999 / Rmerge(I) obs: 0.1398 / Rpim(I) all: 0.0581 / Rrim(I) all: 0.1516 / Net I/σ(I): 12.53 |
Reflection shell | Resolution: 2.227→2.31 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.5265 / Mean I/σ(I) obs: 4.37 / Num. unique obs: 40296 / CC1/2: 0.899 / CC star: 0.973 / Rpim(I) all: 0.2292 / Rrim(I) all: 0.5753 / % possible all: 99.97 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3MUN Resolution: 2.227→44.198 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.925 / SU B: 5.865 / SU ML: 0.145 / Cross valid method: FREE R-VALUE / ESU R: 0.327 / ESU R Free: 0.208 / Details: Hydrogens have not been used
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 21.548 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.227→44.198 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20
|