+Open data
-Basic information
Entry | Database: PDB / ID: 1bk1 | ||||||
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Title | ENDO-1,4-BETA-XYLANASE C | ||||||
Components | ENDO-1,4-B-XYLANASE C | ||||||
Keywords | HYDROLASE / XYLAN DEGRADATION / GLYCOSIDASE | ||||||
Function / homology | Function and homology information endo-1,4-beta-xylanase activity / endo-1,4-beta-xylanase / xylan catabolic process / extracellular region Similarity search - Function | ||||||
Biological species | Aspergillus kawachii (mold) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Fushinobu, S. / Ito, K. / Konno, M. / Wakagi, T. / Matsuzawa, H. | ||||||
Citation | Journal: Protein Eng. / Year: 1998 Title: Crystallographic and mutational analyses of an extremely acidophilic and acid-stable xylanase: biased distribution of acidic residues and importance of Asp37 for catalysis at low pH. Authors: Fushinobu, S. / Ito, K. / Konno, M. / Wakagi, T. / Matsuzawa, H. #1: Journal: Biosci.Biotechnol.Biochem. / Year: 1992 Title: Purification and Properties of Acid Stable Xylanases from Aspergillus Kawachii Authors: Ito, K. / Ogasawara, H. / Sugimoto, T. / Ishikawa, T. #2: Journal: Biosci.Biotechnol.Biochem. / Year: 1992 Title: Cloning and Sequencing of the Xync Gene Encoding Acid Xylanase of Aspergillus Kawachii Authors: Ito, K. / Iwashita, K. / Iwano, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1bk1.cif.gz | 45.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1bk1.ent.gz | 35 KB | Display | PDB format |
PDBx/mmJSON format | 1bk1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bk/1bk1 ftp://data.pdbj.org/pub/pdb/validation_reports/bk/1bk1 | HTTPS FTP |
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-Related structure data
Related structure data | 1xynS 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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Unit cell |
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-Components
#1: Protein | Mass: 19893.988 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aspergillus kawachii (mold) / Strain: IFO 4308 / Cellular location: EXTRACELLULARGlossary of biology / Gene: XYNC / Plasmid: PUAMXC1 / Cellular location (production host): EXTRACELLULAR / Gene (production host): XYNC / Production host: Aspergillus kawachii (mold) / Strain (production host): IFO 4308 / References: UniProt: P33557, 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: 2 |
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-Sample preparation
Crystal | Density Matthews: 2.75 Å3/Da / Density % sol: 55.2 % Description: DATA WERE COLLECTED USING THE WEISSENBERG METHOD | |||||||||||||||||||||||||
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Crystal grow | pH: 6.5 / Details: pH 6.5 | |||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 25 ℃ / pH: 3.5 / Method: vapor diffusion, hanging dropDetails: 0.02ml of protein solution was mixed with 0.01ml of reservoir solution | |||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 1 |
Detector | Type: FUJI / Detector: IMAGE PLATE / Date: Jul 4, 1996 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2→34.7 Å / Num. obs: 15428 / % possible obs: 98.4 % / Observed criterion σ(I): 0.1 / Redundancy: 8.7 % / Biso Wilson estimate: 27.9 Å2 / Rmerge(I) obs: 0.073 / Net I/σ(I): 10.3 |
Reflection shell | Resolution: 2→2.07 Å / Rmerge(I) obs: 0.397 / % possible all: 97.2 |
Reflection | *PLUS Num. measured all: 134544 |
Reflection shell | *PLUS % possible obs: 97.2 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: TRICHODERMA REESEI XYNI, PDB ENTRY 1XYN Resolution: 2→6 Å / Rfactor Rfree error: 0.01 / Cross valid method: THROUGHOUT / σ(F): 3
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Displacement parameters | Biso mean: 30.1 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.27 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→6 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.09 Å / Rfactor Rfree error: 0.032 / Total num. of bins used: 8
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor Rfree: 0.259 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor obs: 0.309 |