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Yorodumi- PDB-1i8u: FAMILY 9 CARBOHYDRATE-BINDING MODULE FROM THERMOTOGA MARITIMA XYL... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1i8u | ||||||
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Title | FAMILY 9 CARBOHYDRATE-BINDING MODULE FROM THERMOTOGA MARITIMA XYLANASE 10A | ||||||
Components | ENDO-1,4-BETA-XYLANASE A | ||||||
Keywords | HYDROLASE / CBM9-2 / CELLULOSE BINDING DOMAIN | ||||||
Function / homology | Function and homology information endo-1,4-beta-xylanase activity / endo-1,4-beta-xylanase / xylan catabolic process / carbohydrate binding Similarity search - Function | ||||||
Biological species | Thermotoga maritima (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MAD / Resolution: 1.9 Å | ||||||
Authors | Notenboom, V. / Boraston, A.B. / Warren, R.A.J. / Kilburn, D.G. / Rose, D.R. | ||||||
Citation | Journal: Biochemistry / Year: 2001 Title: Crystal structures of the family 9 carbohydrate-binding module from Thermotoga maritima xylanase 10A in native and ligand-bound forms. Authors: Notenboom, V. / Boraston, A.B. / Kilburn, D.G. / Rose, D.R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1i8u.cif.gz | 53.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1i8u.ent.gz | 38.1 KB | Display | PDB format |
PDBx/mmJSON format | 1i8u.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i8/1i8u ftp://data.pdbj.org/pub/pdb/validation_reports/i8/1i8u | HTTPS FTP |
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-Related 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: 21329.785 Da / Num. of mol.: 1 / Fragment: C2 DOMAIN (RESIDUES 871-1059) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermotoga maritima (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: Q60037, endo-1,4-beta-xylanase | ||
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#2: Chemical | #3: 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: 2.3 Å3/Da / Density % sol: 46.45 % | ||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: NA ACETATE, P8K, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||
Crystal | *PLUS Density % sol: 43 % | ||||||||||||||||||||
Crystal grow | *PLUS pH: 4.5 | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 15, 1999 / Details: OSMIC MIRROR |
Radiation | Monochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→20 Å / Num. all: 90745 / Num. obs: 90745 / % possible obs: 97.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.8 % / Biso Wilson estimate: 6.3 Å2 / Rmerge(I) obs: 0.065 / Net I/σ(I): 8.8 |
Reflection shell | Resolution: 1.9→2.02 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.047 / Num. unique all: 1514 / % possible all: 63.6 |
Reflection | *PLUS Lowest resolution: 20 Å / Num. obs: 15478 / % possible obs: 97.7 % / Num. measured all: 90745 / Rmerge(I) obs: 0.065 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.9→20 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 296530.27 / Data cutoff low absF: 0 / Isotropic thermal model: OVERALL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: cns
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 59.95 Å2 / ksol: 0.454 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 14.9 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.9→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→2.02 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS σ(F): 0 / % reflection Rfree: 10.1 % | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 14.9 Å2 | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.284 / % reflection Rfree: 10 % / Rfactor Rwork: 0.243 |