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Yorodumi- PDB-1h4g: Oligosaccharide-binding to family 11 xylanases: both covalent int... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1h4g | ||||||||||||
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Title | Oligosaccharide-binding to family 11 xylanases: both covalent intermediate and mutant-product complexes display 2,5B conformations at the active-centre | ||||||||||||
Components | XYLANASE | ||||||||||||
Keywords | GLYCOSIDE HYDROLASE / XYLANASE / OLIGOSACCHARIDE / TRANSITION-STATE / INTERMEDIATE / MUTANT / BOAT CONFORMATION | ||||||||||||
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 AGARADHAERENS (bacteria) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 1.1 Å | ||||||||||||
Authors | Sabini, E. / Wilson, K.S. / Danielsen, S. / Schulein, M. / Davies, G.J. | ||||||||||||
Citation | Journal: Chem.Biol. / Year: 1999 Title: Catalysis and Specificity in Enzymatic Glycoside Hydrolysis: A 2,5B Conformation for the Glycosyl-Enzyme Intermediate Revealed by the Structure of the Bacillus Agaradhaerens Family 11 Xylanase. Authors: Sabini, E. / Sulzenbacher, G. / Dauter, M. / Dauter, Z. / Jorgensen, P.L. / Schulein, M. / Dupont, C. / Davies, G.J. / Wilson, K.S. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1h4g.cif.gz | 194.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1h4g.ent.gz | 159.1 KB | Display | PDB format |
PDBx/mmJSON format | 1h4g.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h4/1h4g ftp://data.pdbj.org/pub/pdb/validation_reports/h4/1h4g | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 23155.547 Da / Num. of mol.: 2 / Fragment: FAMILY 11 XYLANASE CATALYTIC DOMAIN Source method: isolated from a genetically manipulated source Details: 2-FLUORO-2-DEOXY-XYLOBIOSIDE COVALENTLY BOUND TO NUCLEOPHILE GLU94 IN THE ACTIVE SITE Source: (gene. exp.) BACILLUS AGARADHAERENS (bacteria) / Production host: BACILLUS LICHENIFORMIS (bacteria) / References: UniProt: Q7SIE3*PLUS, endo-1,4-beta-xylanase #2: Polysaccharide | Source method: isolated from a genetically manipulated source #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.6 Å3/Da / Density % sol: 53 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 6 Details: DROP: 2UL PROTEIN (10 MG ML-1 IN 100MM SODIUM ACETATE) PLUS 1UL RESERVOIR RESERVOIR: 100 MM MES PH 6.5, 30% AMMONIUM SULPHATE | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 120 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.8469 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8469 Å / Relative weight: 1 |
Reflection | Resolution: 1.1→20 Å / Num. obs: 171783 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Redundancy: 4.5 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 17.6 |
Reflection shell | Resolution: 1.1→1.12 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.708 / Mean I/σ(I) obs: 2 / % possible all: 99 |
Reflection | *PLUS Highest resolution: 1.1 Å / % possible obs: 99.9 % / Rmerge(I) obs: 0.055 |
Reflection shell | *PLUS % possible obs: 99 % / Rmerge(I) obs: 0.71 |
-Processing
Software |
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Refinement | Method to determine structure: OTHER / Resolution: 1.1→20 Å / SU B: 0.38942 / SU ML: 0.01943 / Cross valid method: THROUGHOUT / ESU R Free: 0.03143
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Refinement step | Cycle: LAST / Resolution: 1.1→20 Å
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Refinement | *PLUS Highest resolution: 1.1 Å / Rfactor obs: 0.158 / Rfactor Rfree: 0.18 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS
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