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- PDB-1i82: FAMILY 9 CARBOHYDRATE-BINDING MODULE FROM THERMOTOGA MARITIMA XYL... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1i82 | |||||||||
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Title | FAMILY 9 CARBOHYDRATE-BINDING MODULE FROM THERMOTOGA MARITIMA XYLANASE 10A WITH CELLOBIOSE | |||||||||
![]() | ENDO-1,4-BETA-XYLANASE A | |||||||||
![]() | HYDROLASE / CELLOBIOSE COMPLEX | |||||||||
Function / homology | ![]() endo-1,4-beta-xylanase activity / endo-1,4-beta-xylanase / xylan catabolic process / carbohydrate binding Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() | |||||||||
![]() | Notenboom, V. / Boraston, A.B. / Warren, R.A.J. / Kilburn, D.G. / Rose, D.R. | |||||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 55.2 KB | Display | ![]() |
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PDB format | ![]() | 38.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 417 KB | Display | ![]() |
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Full document | ![]() | 417.5 KB | Display | |
Data in XML | ![]() | 5.3 KB | Display | |
Data in CIF | ![]() | 8.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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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.) ![]() ![]() ![]() ![]() | ||
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#2: Polysaccharide | beta-D-glucopyranose-(1-4)-beta-D-glucopyranose / beta-cellobiose | ||
#3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.31 Å3/Da / Density % sol: 46.83 % | ||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: p8K,Na Acetate, 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: ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 20, 1999 / Details: osmic focus 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: 272755 / Num. obs: 272755 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 15.6 % / Biso Wilson estimate: 6.1 Å2 / Rmerge(I) obs: 0.077 / Net I/σ(I): 9.5 |
Reflection shell | Resolution: 1.9→2.02 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.287 / % possible all: 95.8 |
Reflection | *PLUS Num. obs: 17513 / % possible obs: 99.4 % / Num. measured all: 272755 / Rmerge(I) obs: 0.077 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: Fam9 native Resolution: 1.9→20 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 330467.53 / 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: 42.96 Å2 / ksol: 0.368 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 12 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: 0.018 / 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: 9.8 % | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 12 Å2 | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.267 / % reflection Rfree: 8.7 % / Rfactor Rwork: 0.251 |