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- PDB-2vo5: Structural and biochemical evidence for a boat-like transition st... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2vo5 | ||||||
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Title | Structural and biochemical evidence for a boat-like transition state in beta-mannosidases | ||||||
![]() | BETA-MANNOSIDASE | ||||||
![]() | HYDROLASE / GLYCOSIDE / MANNOSIDASE / TRANSITION STATE MIMIC / LINEAR FREE ENERGY RELATIONSHIP | ||||||
Function / homology | ![]() beta-mannosidase / beta-mannosidase activity / glycoprotein catabolic process / carbohydrate metabolic process / extracellular region Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Tailford, L.E. / Offen, W.A. / Smith, N.L. / Dumon, C. / Moreland, C. / Gratien, J. / Heck, M.P. / Stick, R.V. / Bleriot, Y. / Vasella, A. ...Tailford, L.E. / Offen, W.A. / Smith, N.L. / Dumon, C. / Moreland, C. / Gratien, J. / Heck, M.P. / Stick, R.V. / Bleriot, Y. / Vasella, A. / Gilbert, H.J. / Davies, G.J. | ||||||
![]() | ![]() Title: Structural and Biochemical Evidence for a Boat-Like Transition State in Beta-Mannosidases. Authors: Tailford, L.E. / Offen, W.A. / Smith, N.L. / Dumon, C. / Morland, C. / Gratien, J. / Heck, M.P. / Stick, R.V. / Bleriot, Y. / Vasella, A. / Gilbert, H.J. / 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 | ![]() | 375.5 KB | Display | ![]() |
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PDB format | ![]() | 298.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 68.7 KB | Display | |
Data in CIF | ![]() | 101.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2vjxC ![]() 2vl4C ![]() 2vmfC ![]() 2votC ![]() 2vqtC ![]() 2vquC ![]() 2vr4C ![]() 2je8S C: citing same article ( S: Starting model for refinement |
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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: 97989.727 Da / Num. of mol.: 2 / Fragment: RESIDUES 26-864 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: VPI-5482 / Plasmid: PET28A / Production host: ![]() ![]() |
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-Non-polymers , 5 types, 999 molecules ![](data/chem/img/VBZ.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/BR.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/BR.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | ChemComp-EDO / #4: Chemical | ChemComp-BR / #5: Chemical | ChemComp-CL / #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.5 Å3/Da / Density % sol: 52 % / Description: NONE |
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Crystal grow | Details: 14% PEG 3350, 0.2M NABR, 0.1M MES BUFFER PH 6.4 |
-Data collection
Diffraction | Mean temperature: 120 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC CCD / Detector: CCD / Date: Apr 13, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.934 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→57.83 Å / Num. obs: 84327 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 4.9 % / Rmerge(I) obs: 0.25 / Net I/σ(I): 8 |
Reflection shell | Resolution: 2.3→2.4 Å / Redundancy: 5 % / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 3 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2JE8 Resolution: 2.3→52.49 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.884 / SU B: 6.996 / SU ML: 0.173 / Cross valid method: THROUGHOUT / ESU R: 0.335 / ESU R Free: 0.249 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES 26-27, 848-851 AND 865-871 ARE DISORDERED IN CHAIN A. RESIDUES 26 AND 868-871 ARE DISORDERED IN CHAIN B.
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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 mean: 19.64 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→52.49 Å
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Refine LS restraints |
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