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- PDB-7op7: Bacteroides thetaiotaomicron mannosidase GH2 with beta-manno-conf... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7op7 | ||||||||||||
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Title | Bacteroides thetaiotaomicron mannosidase GH2 with beta-manno-configured N-alkyl cyclophellitol aziridine | ||||||||||||
![]() | Beta-mannosidase | ||||||||||||
![]() | HYDROLASE / mannosidase / cyclophellitol aziridine | ||||||||||||
Function / homology | ![]() beta-mannosidase / beta-mannosidase activity / glycoprotein catabolic process / carbohydrate metabolic process / extracellular region Similarity search - Function | ||||||||||||
Biological species | ![]() | ||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||
![]() | 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 | ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 382.3 KB | Display | ![]() |
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PDB format | ![]() | 301.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1007.6 KB | Display | ![]() |
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Full document | ![]() | 1023.5 KB | Display | |
Data in XML | ![]() | 68.7 KB | Display | |
Data in CIF | ![]() | 101.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7odjC ![]() 7omiC ![]() 7omsC ![]() 7op6C ![]() 2je8S S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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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 his6 tag Source: (gene. exp.) ![]() Gene: BT_0458 / Production host: ![]() ![]() |
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-Non-polymers , 5 types, 889 molecules ![](data/chem/img/EDO.gif)
![](data/chem/img/VEE.gif)
![](data/chem/img/BR.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/VEE.gif)
![](data/chem/img/BR.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-EDO / #3: Chemical | #4: Chemical | ChemComp-BR / #5: Chemical | ChemComp-CL / #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: 2.41 Å3/Da / Density % sol: 49 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.5 / 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: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Apr 25, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97629 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→67.66 Å / Num. obs: 158303 / % possible obs: 99.9 % / Redundancy: 5.5 % / CC1/2: 0.997 / Rpim(I) all: 0.053 / Net I/σ(I): 8.3 |
Reflection shell | Resolution: 1.85→1.88 Å / Mean I/σ(I) obs: 0.7 / Num. unique obs: 7816 / CC1/2: 0.5 / Rpim(I) all: 1.004 / % possible all: 99.8 |
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Processing
Software |
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Refinement | Method to determine structure: ![]() Starting model: 2JE8.pdb Resolution: 1.85→67.66 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.941 / SU B: 5.432 / SU ML: 0.147 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.145 / ESU R Free: 0.145 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY THE ALKYL CHAIN OF THE LIGAND IN MOLECULE A IS MODELLED PARTLY, WITH SOME ATOMS AT PARTIAL OCCUPANCY. THE ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY THE ALKYL CHAIN OF THE LIGAND IN MOLECULE A IS MODELLED PARTLY, WITH SOME ATOMS AT PARTIAL OCCUPANCY. THE LIGAND IN MOLECULE B IS MODELLED AT HALF OCCUPANCY, AND AN ETHYLENE GLYCOL AT HALF OCCUPANCY IS ALSO BOUND IN THE ACTIVE SITE.
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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: 94.07 Å2 / Biso mean: 32.299 Å2 / Biso min: 12.64 Å2
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Refinement step | Cycle: final / Resolution: 1.85→67.66 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.85→1.898 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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