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- PDB-1c5i: HYDROGEN BONDING AND CATALYSIS: AN UNEXPECTED EXPLANATION FOR HOW... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1c5i | |||||||||
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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 | |||||||||
![]() | ENDO-1,4-BETA-XYLANASE | |||||||||
![]() | HYDROLASE / GLYCOSIDASE / PH-DEPENDENT ENZYME MECHANISM / GENERAL ACID/ BASE CATALYSIS / ISOTOPE SHIFT / SHORT HYDROGEN BONDS / XYLAN | |||||||||
Function / homology | ![]() endo-1,4-beta-xylanase activity / endo-1,4-beta-xylanase / xylan catabolic process Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() | |||||||||
![]() | Joshi, M.D. / Sidhu, G. / Pot, I. / Brayer, G.D. / Withers, S.G. / Mcintosh, L.P. | |||||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 51.5 KB | Display | ![]() |
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PDB format | ![]() | 36 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 679 KB | Display | ![]() |
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Full document | ![]() | 678.9 KB | Display | |
Data in XML | ![]() | 10.4 KB | Display | |
Data in CIF | ![]() | 14.4 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: 20409.988 Da / Num. of mol.: 1 / Fragment: CATALYTIC DOMAIN / Mutation: N35D Source method: isolated from a genetically manipulated source Details: 2-DEOXY-2-FLUORO-XYLOBIOSE COVALENTLY BONDED TO GLU 78 OE2 Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Polysaccharide | beta-D-xylopyranose-(1-4)-1,5-anhydro-2-deoxy-2-fluoro-D-xylitol Source method: isolated from a genetically manipulated source |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.23 Å3/Da / Density % sol: 44.86 % | ||||||||||||||||||||||||||||||
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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: ![]() |
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: 1.8→50 Å / Num. obs: 17579 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 5.6 % / Rmerge(I) obs: 0.073 / Net I/σ(I): 25.8 |
Reflection | *PLUS Lowest resolution: 9999 Å / Num. measured all: 99311 |
Reflection shell | *PLUS Highest resolution: 1.8 Å / Lowest resolution: 1.86 Å / Rmerge(I) obs: 0.142 / Mean I/σ(I) obs: 11.1 |
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Processing
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Refinement | Method to determine structure: OTHER / Resolution: 1.8→10 Å / σ(F): 0
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Refinement step | Cycle: LAST / Resolution: 1.8→10 Å
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Refine LS restraints |
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Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 1.8 Å / Lowest resolution: 10 Å / σ(F): 0 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |