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Yorodumi- PDB-1knm: Streptomyces lividans Xylan Binding Domain cbm13 in Complex with ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1knm | |||||||||
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Title | Streptomyces lividans Xylan Binding Domain cbm13 in Complex with Lactose | |||||||||
Components | ENDO-1,4-BETA-XYLANASE A | |||||||||
Keywords | HYDROLASE / xylanase A xylan binding domain cbm13 / lectin-like beta trefoil fold / lactose complex | |||||||||
Function / homology | Function and homology information endo-1,4-beta-xylanase activity / endo-1,4-beta-xylanase / xylan catabolic process / carbohydrate binding / extracellular region Similarity search - Function | |||||||||
Biological species | Streptomyces lividans (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å | |||||||||
Authors | Notenboom, V. / Boraston, A.B. / Williams, S.J. / Kilburn, D.G. / Rose, D.R. | |||||||||
Citation | Journal: Biochemistry / Year: 2002 Title: High-resolution crystal structures of the lectin-like xylan binding domain from Streptomyces lividans xylanase 10A with bound substrates reveal a novel mode of xylan binding. Authors: Notenboom, V. / Boraston, A.B. / Williams, S.J. / 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 | 1knm.cif.gz | 40.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1knm.ent.gz | 30 KB | Display | PDB format |
PDBx/mmJSON format | 1knm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kn/1knm ftp://data.pdbj.org/pub/pdb/validation_reports/kn/1knm | 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: 13608.731 Da / Num. of mol.: 1 / Fragment: carbohydrate binding module (residues 348-477) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces lividans (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: P26514, endo-1,4-beta-xylanase | ||||
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#2: Polysaccharide | #3: Chemical | ChemComp-GOL / | #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: 2.07 Å3/Da / Density % sol: 40.56 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 300 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 1.8 mM Ammonium Sulfate, 50 mM MES pH 6.5, 5% dioxane, VAPOR DIFFUSION, HANGING DROP, temperature 300K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion | ||||||||||||||||||||||||||||||
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: APS / Beamline: 14-BM-D / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 19, 2000 |
Radiation | Monochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.2→1.24 Å / Num. obs: 30016 / % possible obs: 83.1 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 |
Reflection shell | Highest resolution: 1.2 Å / % possible all: 83.1 |
Reflection | *PLUS Num. all: 126516 / Rmerge(I) obs: 0.041 |
Reflection shell | *PLUS % possible obs: 22.1 % / Rmerge(I) obs: 0.193 / Mean I/σ(I) obs: 9.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.2→19.57 Å / σ(F): 0 / Stereochemistry target values: refmac5
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Refinement step | Cycle: LAST / Resolution: 1.2→19.57 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.2→1.24 Å /
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Refinement | *PLUS % reflection Rfree: 5 % | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rwork: 0.23 |