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Yorodumi- PDB-2vjx: Structural and biochemical evidence for a boat-like transition st... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2vjx | ||||||
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Title | Structural and biochemical evidence for a boat-like transition state in beta-mannosidases | ||||||
Components | BETA-MANNOSIDASE | ||||||
Keywords | HYDROLASE / LINEAR FREE ENERGY RELATIONSHIP / TRANSITION STATE MIMIC / MANNOSIDASE / GLYCOSIDE HYDROLASE | ||||||
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 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å | ||||||
Authors | 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. | ||||||
Citation | Journal: Nat.Chem.Biol. / Year: 2008 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. / Moreland, 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2vjx.cif.gz | 385.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2vjx.ent.gz | 306.6 KB | Display | PDB format |
PDBx/mmJSON format | 2vjx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2vjx_validation.pdf.gz | 487.3 KB | Display | wwPDB validaton report |
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Full document | 2vjx_full_validation.pdf.gz | 499.6 KB | Display | |
Data in XML | 2vjx_validation.xml.gz | 71.1 KB | Display | |
Data in CIF | 2vjx_validation.cif.gz | 108.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vj/2vjx ftp://data.pdbj.org/pub/pdb/validation_reports/vj/2vjx | HTTPS FTP |
-Related structure data
Related structure data | 2vl4C 2vmfC 2vo5C 2votC 2vqtC 2vquC 2vr4C 2je8S C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-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: 97989.727 Da / Num. of mol.: 2 / Fragment: RESIDUES 26-864 Source method: isolated from a genetically manipulated source Source: (gene. exp.) BACTEROIDES THETAIOTAOMICRON (bacteria) Strain: VPI-5482 / Plasmid: PET28A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: Q8AAK6, beta-mannosidase |
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-Non-polymers , 5 types, 1331 molecules
#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: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.5 Å3/Da / Density % sol: 50 % / Description: NONE |
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Crystal grow | Details: 14% PEG 3350, 0.2M NABR, 0.1M MES PH 6.5 |
-Data collection
Diffraction | Mean temperature: 120 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.0004 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Mar 17, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0004 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→83.92 Å / Num. obs: 160278 / % possible obs: 98.8 % / Observed criterion σ(I): 2 / Redundancy: 3.7 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 12.1 |
Reflection shell | Resolution: 1.85→1.9 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.24 / Mean I/σ(I) obs: 4.8 / % possible all: 97.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2JE8 Resolution: 1.85→71.8 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.937 / SU B: 2.405 / SU ML: 0.075 / Cross valid method: THROUGHOUT / ESU R: 0.125 / ESU R Free: 0.121 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUE 318 IS DISORDERED IN CHAIN A, AS ARE 865 - 871. RESIDUES 867-871 ARE DISORDERED IN CHAIN B. RESIDUES 26 AND 27 ARE DISORDERED IN BOTH CHAINS.
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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: 18.01 Å2
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Refinement step | Cycle: LAST / Resolution: 1.85→71.8 Å
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Refine LS restraints |
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