+Open data
-Basic information
Entry | Database: PDB / ID: 2v3g | ||||||
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Title | Structure of a family 26 lichenase in complex with noeuromycin | ||||||
Components | ENDOGLUCANASE H | ||||||
Keywords | HYDROLASE / BETA-1 4 BETA-1 3 GLUCANASE / LICHENASE / GLYCOSIDASE / GLYCOSIDE HYDROLASE FAMILY 26 / POLYSACCHARIDE DEGRADATION / CELLULOSE DEGRADATION / CARBOHYDRATE METABOLISM | ||||||
Function / homology | Function and homology information cellulase / cellulase activity / beta-glucosidase activity / cellulose catabolic process / cell surface / extracellular region Similarity search - Function | ||||||
Biological species | CLOSTRIDIUM THERMOCELLUM (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å | ||||||
Authors | Meloncelli, P.J. / Gloster, T.M. / Money, V.A. / Tarling, C.A. / Davies, G.J. / Withers, S.G. / Stick, R.V. | ||||||
Citation | Journal: To be Published Title: D-Glucosylated Derivatives of Isofagomine and Noeuromycin and Their Potential as Inhibitors of Beta-Glycoside Hydrolases Authors: Meloncelli, P.J. / Gloster, T.M. / Money, V.A. / Tarling, C.A. / Davies, G.J. / Withers, S.G. / Stick, R.V. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2v3g.cif.gz | 145.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2v3g.ent.gz | 113.5 KB | Display | PDB format |
PDBx/mmJSON format | 2v3g.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2v3g_validation.pdf.gz | 457.1 KB | Display | wwPDB validaton report |
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Full document | 2v3g_full_validation.pdf.gz | 459.6 KB | Display | |
Data in XML | 2v3g_validation.xml.gz | 17.5 KB | Display | |
Data in CIF | 2v3g_validation.cif.gz | 28.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v3/2v3g ftp://data.pdbj.org/pub/pdb/validation_reports/v3/2v3g | HTTPS FTP |
-Related structure data
Related structure data | 2v38C 2bv9S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 32174.545 Da / Num. of mol.: 1 / Fragment: CATALYTIC DOMAIN, RESIDUES 26-305 Source method: isolated from a genetically manipulated source Source: (gene. exp.) CLOSTRIDIUM THERMOCELLUM (bacteria) / Strain: F1/YS / Plasmid: PCF1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P16218, cellulase |
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#2: Sugar | ChemComp-BGC / |
#3: Chemical | ChemComp-NOY / ( |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.9 Å3/Da / Density % sol: 36 % / Description: NONE |
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Crystal grow | pH: 6.5 Details: CO-CRYSTALLIZED WITH THE LIGAND FROM 0.15 M AMMONIUM SULPHATE, 30% PEG 5K MME BUFFERED TO PH 6.5 WITH MES AND SEEDED |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.9333 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Apr 8, 2006 / Details: TOROIDAL MIRROR |
Radiation | Monochromator: DIAMOND (111), GE(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9333 Å / Relative weight: 1 |
Reflection | Resolution: 1.2→27.4 Å / Num. obs: 78233 / % possible obs: 98 % / Observed criterion σ(I): 1 / Redundancy: 4.3 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 21.6 |
Reflection shell | Resolution: 1.2→1.26 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.11 / Mean I/σ(I) obs: 9.7 / % possible all: 98 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2BV9 Resolution: 1.2→49.33 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.968 / SU B: 0.84 / SU ML: 0.018 / Cross valid method: THROUGHOUT / ESU R: 0.035 / ESU R Free: 0.035 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 6.4 Å2
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Refinement step | Cycle: LAST / Resolution: 1.2→49.33 Å
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Refine LS restraints |
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