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Yorodumi- PDB-1nae: Structure of CsCBM6-3 from Clostridium stercorarium in complex wi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1nae | |||||||||
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Title | Structure of CsCBM6-3 from Clostridium stercorarium in complex with xylotriose | |||||||||
Components | putative xylanase | |||||||||
Keywords | HYDROLASE / carbohydrate-binding module / beta-sandwich / xylan / xylooligosaccharide | |||||||||
Function / homology | Function and homology information endo-1,4-beta-xylanase activity / endo-1,4-beta-xylanase / xylan catabolic process / cellulose catabolic process / carbohydrate binding / extracellular region / metal ion binding Similarity search - Function | |||||||||
Biological species | Clostridium stercorarium (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.05 Å | |||||||||
Authors | Boraston, A.B. / Notenboom, V. / Warren, R.A.J. / Kilburn, D.G. / Rose, D.R. / Davies, G. | |||||||||
Citation | Journal: J.Mol.Biol. / Year: 2003 Title: Structure and ligand binding of carbohydrate-binding module CsCBM6-3 reveals similarities with fucose-specific lectins and "galactose-binding" domains Authors: Boraston, A.B. / Notenboom, V. / Warren, R.A.J. / Kilburn, D.G. / Rose, D.R. / Davies, G. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1nae.cif.gz | 45 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1nae.ent.gz | 28.9 KB | Display | PDB format |
PDBx/mmJSON format | 1nae.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1nae_validation.pdf.gz | 706.8 KB | Display | wwPDB validaton report |
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Full document | 1nae_full_validation.pdf.gz | 707.6 KB | Display | |
Data in XML | 1nae_validation.xml.gz | 9.5 KB | Display | |
Data in CIF | 1nae_validation.cif.gz | 13.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/na/1nae ftp://data.pdbj.org/pub/pdb/validation_reports/na/1nae | HTTPS FTP |
-Related structure data
Related structure data | 1o8pC 1o8sC 1od3C 1gmmS 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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-Components
#1: Protein | Mass: 17405.947 Da / Num. of mol.: 1 / Fragment: C-terminal carbohydrate-binding module Source method: isolated from a genetically manipulated source Source: (gene. exp.) Clostridium stercorarium (bacteria) / Gene: putative xylanase / Plasmid: pET28a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21/DE3 / References: GenBank: 16076818, UniProt: Q8GJ44*PLUS |
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#2: Polysaccharide | beta-D-xylopyranose-(1-4)-beta-D-xylopyranose-(1-4)-beta-D-xylopyranose / 4beta-beta-xylotriose |
#3: Chemical | ChemComp-CA / |
#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: 1.63 Å3/Da / Density % sol: 24.09 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: 26%PEG 4K, 0.1 M sodium acetate, pH 4.6, 0.2 M ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 291K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS | ||||||||||||||||||||||||||||||
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: Jul 12, 2002 / Details: long mirror focused |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.05→36.04 Å / Num. all: 6680 / Num. obs: 6382 / Redundancy: 2.3 % / Biso Wilson estimate: 20.33 Å2 / Rmerge(I) obs: 0.07 / Rsym value: 0.07 / Net I/σ(I): 12.4 |
Reflection shell | Resolution: 2.05→2.12 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.186 / Mean I/σ(I) obs: 5.4 / Num. unique all: 649 / Rsym value: 0.186 |
Reflection | *PLUS Highest resolution: 2.25 Å / Lowest resolution: 40 Å / % possible obs: 94.6 % / Redundancy: 8.5 % / Rmerge(I) obs: 0.046 |
Reflection shell | *PLUS Highest resolution: 2.25 Å / Lowest resolution: 2.36 Å / % possible obs: 72.1 % / Redundancy: 5 % / Rmerge(I) obs: 0.141 / Mean I/σ(I) obs: 6.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1gmm Resolution: 2.05→36.04 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.946 / SU B: 4.63 / SU ML: 0.126 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R: 0.334 / ESU R Free: 0.194
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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: 19.907 Å2
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Refinement step | Cycle: LAST / Resolution: 2.05→36.04 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.05→2.103 Å / Total num. of bins used: 20
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Refinement | *PLUS Highest resolution: 2.25 Å / Lowest resolution: 40 Å / Rfactor Rfree: 0.203 / Rfactor Rwork: 0.161 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Highest resolution: 2.25 Å / Lowest resolution: 2.36 Å |