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Yorodumi- PDB-1h4h: Oligosaccharide-binding to family 11 xylanases: both covalent int... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1h4h | ||||||||||||
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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 / MOLECULAR REPLACEMENT / Resolution: 1.9 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 | 1h4h.cif.gz | 185.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1h4h.ent.gz | 147.1 KB | Display | PDB format |
PDBx/mmJSON format | 1h4h.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1h4h_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 1h4h_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 1h4h_validation.xml.gz | 41 KB | Display | |
Data in CIF | 1h4h_validation.cif.gz | 56.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h4/1h4h ftp://data.pdbj.org/pub/pdb/validation_reports/h4/1h4h | HTTPS FTP |
-Related structure data
Related structure data | 1h4gC 1qh6SC 1qh7C C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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4 |
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Unit cell |
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-Components
#1: Protein | Mass: 23311.773 Da / Num. of mol.: 4 / Fragment: FAMILY 11 XYLANASE CATALYTIC DOMAIN / Mutation: YES Source method: isolated from a genetically manipulated source Details: XYLOTRIOSE IN THE ACTIVE SITE / Source: (gene. exp.) BACILLUS AGARADHAERENS (bacteria) / Production host: BACILLUS LICHENIFORMIS (bacteria) / References: UniProt: Q7SIE2*PLUS, endo-1,4-beta-xylanase #2: Polysaccharide | beta-D-xylopyranose-(1-4)-beta-D-xylopyranose-(1-4)-alpha-D-xylopyranose Source method: isolated from a genetically manipulated source #3: Water | ChemComp-HOH / | Compound details | CHAIN A, B, C, D ENGINEERED | |
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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: 2.8 Å3/Da / Density % sol: 56 % | |||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 6.5 Details: DROP: 1UL PROTEIN (27 MG ML-1) PLUS 1UL RESERVOIR RESERVOIR: 100 MM MES PH 6.5, 0.8M K2HPO4.3H20/NAH2PO4, 10% MPD | |||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 289 K / 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: ESRF / Beamline: ID14-4 / 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: 1.9→20 Å / Num. obs: 53623 / % possible obs: 77.5 % / Observed criterion σ(I): 2 / Redundancy: 4.6 % / Rmerge(I) obs: 0.051 / Net I/σ(I): 21.5 |
Reflection shell | Resolution: 1.9→1.93 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.157 / Mean I/σ(I) obs: 5 / % possible all: 23.9 |
Reflection | *PLUS Highest resolution: 1.9 Å / % possible obs: 77.7 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1QH6 Resolution: 1.9→20 Å / SU B: 4.86098 / SU ML: 0.13461 / Cross valid method: THROUGHOUT / ESU R Free: 0.19035
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Refinement step | Cycle: LAST / Resolution: 1.9→20 Å
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Refinement | *PLUS Rfactor obs: 0.18 / Rfactor Rfree: 0.24 / Rfactor Rwork: 0.18 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.32 / Rfactor Rwork: 0.22 / Rfactor obs: 0.22 |