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Yorodumi- PDB-1tyj: Crystal Structure Analysis of type II Cohesin A11 from Bacteroide... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1tyj | ||||||
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Title | Crystal Structure Analysis of type II Cohesin A11 from Bacteroides cellulosolvens | ||||||
Components | cellulosomal scaffoldin | ||||||
Keywords | STRUCTURAL PROTEIN / beta sandwich / dockerin-binding module / alpha helix / flaps | ||||||
Function / homology | Function and homology information cellulose binding / polysaccharide catabolic process / hydrolase activity, hydrolyzing O-glycosyl compounds / extracellular region Similarity search - Function | ||||||
Biological species | Bacteroides cellulosolvens (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||
Authors | Noach, I. / Frolow, F. / Jakoby, H. / Rosenheck, S. / Shimon, L.J.W. / Lamed, R. / Bayer, E.A. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2005 Title: Crystal structure of a type-II cohesin module from the Bacteroides cellulosolvens cellulosome reveals novel and distinctive secondary structural elements Authors: Noach, I. / Frolow, F. / Jakoby, H. / Rosenheck, S. / Shimon, L.J.W. / Lamed, R. / Bayer, E.A. #1: Journal: Acta Crystallogr.,Sect.D / Year: 2003 Title: Preliminary X-ray characterization and phasing of a type II cohesin domain from the cellulosome of Acetivibrio cellulolyticus Authors: Noach, I. / Lamed, R. / Xu, Q. / Rosenheck, S. / Shimon, L.J.W. / Bayer, E.A. / Frolow, F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1tyj.cif.gz | 89.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1tyj.ent.gz | 67.6 KB | Display | PDB format |
PDBx/mmJSON format | 1tyj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1tyj_validation.pdf.gz | 443.4 KB | Display | wwPDB validaton report |
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Full document | 1tyj_full_validation.pdf.gz | 444.3 KB | Display | |
Data in XML | 1tyj_validation.xml.gz | 11.5 KB | Display | |
Data in CIF | 1tyj_validation.cif.gz | 16.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ty/1tyj ftp://data.pdbj.org/pub/pdb/validation_reports/ty/1tyj | HTTPS FTP |
-Related structure data
Related structure data | 1qznSC 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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Details | The asymmetric unit of the crystal structure contains a single biological unit |
-Components
#1: Protein | Mass: 18669.943 Da / Num. of mol.: 1 / Fragment: type-II cohesin domain 11 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacteroides cellulosolvens (bacteria) / Gene: CipBc(ScaA) / Plasmid: pET28a / Species (production host): Escherichia coli / Cellular location (production host): cellulosome / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: GenBank: 34223562, UniProt: Q9FDJ9*PLUS | ||||
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#2: Chemical | ChemComp-EDO / #3: Chemical | ChemComp-MOH / | #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: 2.29 Å3/Da / Density % sol: 45.85 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 0.1M Tris hydrochloride, ammonium sulfate, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.933 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Jun 20, 2001 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→72.55 Å / Num. all: 26333 / Num. obs: 26333 / % possible obs: 97.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.94 % / Biso Wilson estimate: 19.82 Å2 / Rmerge(I) obs: 0.036 / Rsym value: 0.036 / Net I/σ(I): 19.9 |
Reflection shell | Resolution: 1.6→1.64 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.26 / Mean I/σ(I) obs: 3.9 / Num. unique all: 1739 / Rsym value: 0.26 / % possible all: 93.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1QZN Resolution: 1.6→72.55 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.958 / SU B: 1.427 / SU ML: 0.05 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): -3 / ESU R: 0.105 / ESU R Free: 0.082 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.505 Å2
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Refinement step | Cycle: LAST / Resolution: 1.6→72.55 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.6→1.642 Å / Total num. of bins used: 20
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