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Yorodumi- PDB-1c5h: HYDROGEN BONDING AND CATALYSIS: AN UNEXPECTED EXPLANATION FOR HOW... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1c5h | ||||||
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Title | HYDROGEN BONDING AND CATALYSIS: AN UNEXPECTED EXPLANATION FOR HOW A SINGLE AMINO ACID SUBSTITUTION CAN CHANGE THE PH OPTIMUM OF A GLYCOSIDASE | ||||||
Components | ENDO-1,4-BETA-XYLANASEXylanase | ||||||
Keywords | HYDROLASE / GLYCOSIDASE / PH-DEPENDENT ENZYME MECHANISM / GENERAL ACID/ BASE CATALYSIS / X-RAY CYRSTALLOGRAPHY / ISOTOPE SHIFT / SHORT HYDROGEN BONDS / XYLAN | ||||||
Function / homology | Function and homology information endo-1,4-beta-xylanase activity / endo-1,4-beta-xylanase / xylan catabolic process Similarity search - Function | ||||||
Biological species | Bacillus circulans (bacteria) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 1.55 Å | ||||||
Authors | Joshi, M.D. / Sidhu, G. / Pot, I. / Brayer, G.D. / Withers, S.G. / Mcintosh, L.P. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2000 Title: Hydrogen bonding and catalysis: a novel explanation for how a single amino acid substitution can change the pH optimum of a glycosidase. Authors: Joshi, M.D. / Sidhu, G. / Pot, I. / Brayer, G.D. / Withers, S.G. / McIntosh, L.P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1c5h.cif.gz | 49.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1c5h.ent.gz | 35.5 KB | Display | PDB format |
PDBx/mmJSON format | 1c5h.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c5/1c5h ftp://data.pdbj.org/pub/pdb/validation_reports/c5/1c5h | 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: 20409.988 Da / Num. of mol.: 1 / Fragment: CATALYTIC DOMAIN / Mutation: N35D Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus circulans (bacteria) / Plasmid: PCW / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P09850, endo-1,4-beta-xylanase |
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#2: 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: 2.23 Å3/Da / Density % sol: 44.95 % | ||||||||||||||||||||||||||||||
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Crystal grow | pH: 7.5 / Details: pH 7.5 | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop / Details: Sidhu, G., (1999) J. Mol. Biol., 38, 5346. | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.55→50 Å / Num. obs: 27301 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 5.5 % / Rmerge(I) obs: 0.057 / Net I/σ(I): 21.1 |
Reflection | *PLUS Highest resolution: 1.55 Å / Lowest resolution: 9999 Å / Observed criterion σ(I): 0 / Redundancy: 5.5 % / Num. measured all: 150984 |
Reflection shell | *PLUS Highest resolution: 1.55 Å / Lowest resolution: 1.61 Å / Rmerge(I) obs: 0.152 / Mean I/σ(I) obs: 7 |
-Processing
Software |
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Refinement | Resolution: 1.55→10 Å / σ(F): 0
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Refinement step | Cycle: LAST / Resolution: 1.55→10 Å
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Refine LS restraints |
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