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Yorodumi- PDB-1gmm: Carbohydrate binding module CBM6 from xylanase U Clostridium ther... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1gmm | ||||||
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Title | Carbohydrate binding module CBM6 from xylanase U Clostridium thermocellum | ||||||
Components | CBM6Midway Aerodrome | ||||||
Keywords | XYLANASE / CARBOHYDRATE BINDING MODULE / CBM FAMILY 6 / XYLAN BINDING | ||||||
Function / homology | Function and homology information hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds / endo-1,4-beta-xylanase activity / endo-1,4-beta-xylanase / xylan catabolic process / carbohydrate binding / metal ion binding Similarity search - Function | ||||||
Biological species | CLOSTRIDIUM THERMOCELLUM (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å | ||||||
Authors | Czjzek, M. / Mosbah, A. / Bolam, D. / Allouch, J. / Zamboni, V. / Henrissat, B. / Gilbert, H.J. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2001 Title: The Location of the Ligand-Binding Site of Carbohydrate-Binding Modules that Have Evolved from a Common Sequence is not Conserved. Authors: Czjzek, M. / Bolam, D. / Mosbah, A. / Allouch, J. / Fontes, C.M. / Ferreira, L.M. / Bornet, O. / Zamboni, V. / Darbon, H. / Smith, N.L. / Black, G.W. / Henrissat, B. / Gilbert, H.J. #1: Journal: Biochem.J. / Year: 1999 Title: Homologous Xylanases from Clostridium Thermocellum: Evidence for Bi-Functional Activity, Synergism between Xylanase Catalytic Modules and the Presence of Xylan-Binding Domains in Enzyme Complexes Authors: Fernandes, A. / Fontes, C.M.G.A. / Gilbert, H.J. / Hazelwood, G.P. / Fernandes, T.H. / Ferreira, L.M.A. / Gilbert, H.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1gmm.cif.gz | 38.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1gmm.ent.gz | 29.5 KB | Display | PDB format |
PDBx/mmJSON format | 1gmm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gm/1gmm ftp://data.pdbj.org/pub/pdb/validation_reports/gm/1gmm | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 14115.347 Da / Num. of mol.: 1 / Fragment: XYLAN BINDING MODULE (DOMAIN), RESIDUE 248-380 Source method: isolated from a genetically manipulated source Source: (gene. exp.) CLOSTRIDIUM THERMOCELLUM (bacteria) / Strain: F1 / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: O52780, endo-1,4-beta-xylanase |
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#2: Chemical | ChemComp-SO4 / |
#3: Chemical | ChemComp-NA / |
#4: Chemical | ChemComp-CA / |
#5: 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: 2.73 Å3/Da / Density % sol: 55 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 5.5 Details: 30% PEG 4000, 100MM NA-CITRATE PH 5.5, 100MM (NH4)2SO4 | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / pH: 5 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9793, 0.9795, 0.9465, 0.933 | |||||||||||||||
Detector | Detector: CCD / Date: Dec 15, 2000 / Details: MIRRORS | |||||||||||||||
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2→39.22 Å / Num. obs: 11981 / % possible obs: 99.3 % / Observed criterion σ(I): 0.01 / Redundancy: 6.6 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 9.3 | |||||||||||||||
Reflection shell | Resolution: 2→2.11 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.204 / Mean I/σ(I) obs: 1.2 / % possible all: 98.2 | |||||||||||||||
Reflection | *PLUS Rmerge(I) obs: 0.055 | |||||||||||||||
Reflection shell | *PLUS % possible obs: 98.2 % |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2→39 Å / SU B: 3.345 / SU ML: 0.095 / Cross valid method: THROUGHOUT / σ(F): 0.01 / ESU R Free: 0.142 Details: TLS REFINEMENT WAS PERFORMED ON 6 GROUPS. FOUR RESIDUES, THR A 65, THR A 67, SER A 99 AND THR A 103 HAVE BEEN MODELED WITH MULTIPLE ALTERNATE CONFORMATIONS.
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Refinement step | Cycle: LAST / Resolution: 2→39 Å
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Refinement | *PLUS Highest resolution: 2.1 Å / Lowest resolution: 32 Å / Rfactor obs: 0.2 / Rfactor Rfree: 0.216 / Rfactor Rwork: 0.2 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS
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