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Yorodumi- PDB-7op6: Bacteroides thetaiotaomicron mannosidase GH2 with beta-manno-conf... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7op6 | ||||||||||||
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Title | Bacteroides thetaiotaomicron mannosidase GH2 with beta-manno-configured cyclophellitol aziridine | ||||||||||||
Components | Beta-mannosidase | ||||||||||||
Keywords | HYDROLASE / mannosidase / cyclophellitol aziridine | ||||||||||||
Function / homology | Function and homology information beta-mannosidase / beta-mannosidase activity / glycoprotein catabolic process / carbohydrate metabolic process / extracellular region Similarity search - Function | ||||||||||||
Biological species | Bacteroides thetaiotaomicron VPI-5482 (bacteria) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å | ||||||||||||
Authors | McGregor, N.G.S. / Beenakker, T.J.M. / Kuo, C. / Wong, C. / Offen, W.A. / Armstrong, Z. / Codee, J.D.C. / Aerts, J.M.F.G. / Florea, B.I. / Overkleeft, H.S. / Davies, G.J. | ||||||||||||
Funding support | United Kingdom, European Union, 3items
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Citation | Journal: Org.Biomol.Chem. / Year: 2022 Title: Synthesis of broad-specificity activity-based probes for exo -beta-mannosidases. Authors: McGregor, N.G.S. / Kuo, C.L. / Beenakker, T.J.M. / Wong, C.S. / Offen, W.A. / Armstrong, Z. / Florea, B.I. / Codee, J.D.C. / Overkleeft, H.S. / Aerts, J.M.F.G. / Davies, G.J. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7op6.cif.gz | 379.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7op6.ent.gz | 298.5 KB | Display | PDB format |
PDBx/mmJSON format | 7op6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7op6_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 7op6_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 7op6_validation.xml.gz | 66.7 KB | Display | |
Data in CIF | 7op6_validation.cif.gz | 99.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/op/7op6 ftp://data.pdbj.org/pub/pdb/validation_reports/op/7op6 | HTTPS FTP |
-Related structure data
Related structure data | 7odjC 7omiC 7omsC 7op7C 2je8S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 98291.125 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: beta-mannosidase without signal peptide sequence and with C-terminal hexa-his tag Source: (gene. exp.) Bacteroides thetaiotaomicron VPI-5482 (bacteria) Gene: BT_0458 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8AAK6 |
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-Non-polymers , 8 types, 962 molecules
#2: Chemical | ChemComp-BR / #3: Chemical | ChemComp-EDO / #4: Chemical | ChemComp-CL / #5: Chemical | #6: Chemical | ChemComp-JIW / | #7: Chemical | ChemComp-JIT / | #8: Chemical | ChemComp-VKH / ( | #9: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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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: 2.51 Å3/Da / Density % sol: 51.07 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.7 / Details: PEG 3350, sodium bromide, MES buffer |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92819 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jun 19, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.92819 Å / Relative weight: 1 |
Reflection | Resolution: 2.05→92.19 Å / Num. obs: 119933 / % possible obs: 98.6 % / Redundancy: 4.1 % / CC1/2: 0.997 / Rpim(I) all: 0.049 / Net I/σ(I): 8.9 |
Reflection shell | Resolution: 2.05→2.09 Å / Redundancy: 4 % / Num. unique obs: 5880 / CC1/2: 0.535 / Rpim(I) all: 0.522 / % possible all: 97.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2JE8 Resolution: 2.05→92.19 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.937 / SU B: 5.387 / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.202 / ESU R Free: 0.176 / 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: 91.93 Å2 / Biso mean: 33.93 Å2 / Biso min: 12.33 Å2
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Refinement step | Cycle: final / Resolution: 2.05→92.19 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.05→2.103 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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