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Yorodumi- PDB-1h6y: The role of conserved amino acids in the cleft of the C-terminal ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1h6y | ||||||
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Title | The role of conserved amino acids in the cleft of the C-terminal family 22 carbohydrate binding module of Clostridium thermocellum Xyn10B in ligand binding | ||||||
Components | ENDO-1,4-BETA-XYLANASE Y | ||||||
Keywords | HYDROLASE / XYLAN DEGRADATION / GLYCOSIDASE | ||||||
Function / homology | Function and homology information cellulosome / endo-1,4-beta-xylanase activity / endo-1,4-beta-xylanase / xylan catabolic process Similarity search - Function | ||||||
Biological species | CLOSTRIDIUM THERMOCELLUM (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Xie, H. / Bolam, D.N. / Charnock, S.J. / Davies, G.J. / Williamson, M.P. / Simpson, P.J. / Fontes, C.M.G.A. / Ferreira, L.M.A. / Gilbert, H.J. | ||||||
Citation | Journal: Biochemistry / Year: 2001 Title: Clostridium Thermocellum Xyn10B Carbohydrate-Binding Module 22-2: The Role of Conserved Amino Acids in Ligand Binding Authors: Xie, H. / Gilbert, H.J. / Charnock, S.J. / Davies, G.J. / Williamson, M.P. / Simpson, P.J. / Raghothama, S. / Fontes, C.M.G.A. / Dias, F.M. / Ferreira, L.M.A. / Bolam, D.N. #1: Journal: Biochemistry / Year: 2000 Title: The X6 "Thermostabilizing" Domains of Xylanases are Carbohydrate-Binding Modules:Structure and Biochemistry of the Clostridium Thermocellum X6B Domain Authors: Charnock, S.J. / Bolam, D.N. / Turkenburg, J.P. / Gilbert, H.J. / Ferreira, L.M.A. / Davies, G.J. / Fontes, C.M.G.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1h6y.cif.gz | 80.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1h6y.ent.gz | 60.6 KB | Display | PDB format |
PDBx/mmJSON format | 1h6y.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1h6y_validation.pdf.gz | 424.2 KB | Display | wwPDB validaton report |
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Full document | 1h6y_full_validation.pdf.gz | 425 KB | Display | |
Data in XML | 1h6y_validation.xml.gz | 16.8 KB | Display | |
Data in CIF | 1h6y_validation.cif.gz | 24.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h6/1h6y ftp://data.pdbj.org/pub/pdb/validation_reports/h6/1h6y | HTTPS FTP |
-Related structure data
Related structure data | 1h6xC 1dyoS 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 18939.848 Da / Num. of mol.: 2 / Fragment: XYLAN BINDING DOMAIN RESIDUE 560-720 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) CLOSTRIDIUM THERMOCELLUM (bacteria) / Strain: YS / Plasmid: PET21A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: P51584 #2: Chemical | #3: Water | ChemComp-HOH / | Compound details | CHAIN A ENGINEERED | |
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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: 3.22 Å3/Da / Density % sol: 61.75 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 4.6 Details: 0.1 M NAAC(PH 4.6),10 MM DTT, 25% GLYCEROL,12% PEG8000 | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop / pH: 4.6 | ||||||||||||||||||||||||||||||||||||||||||
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: ID14-1 / Wavelength: 0.934 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jul 15, 2000 / Details: FOCUSING AND MULTILAYER |
Radiation | Monochromator: GE(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.934 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→25 Å / Num. obs: 26510 / % possible obs: 99.9 % / Observed criterion σ(I): 3 / Redundancy: 28.3 % / Rmerge(I) obs: 0.068 / Net I/σ(I): 24 |
Reflection shell | Resolution: 2.2→2.28 Å / Redundancy: 25.5 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 5.8 / % possible all: 100 |
Reflection | *PLUS Lowest resolution: 25 Å |
Reflection shell | *PLUS % possible obs: 100 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1DYO Resolution: 2.2→25 Å / Cross valid method: THROUGHOUT / σ(F): 3
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Refinement step | Cycle: LAST / Resolution: 2.2→25 Å
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Refinement | *PLUS Lowest resolution: 25 Å / Rfactor Rwork: 0.192 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS
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