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Yorodumi- PDB-2xyl: CELLULOMONAS FIMI XYLANASE/CELLULASE COMPLEXED WITH 2-DEOXY-2-FLU... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2xyl | |||||||||
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Title | CELLULOMONAS FIMI XYLANASE/CELLULASE COMPLEXED WITH 2-DEOXY-2-FLUORO-XYLOBIOSE | |||||||||
Components | BETA-1,4-GLYCANASE | |||||||||
Keywords | HYDROLASE / O-GLYCOSYL / XYLANASE/CELLULASE / A/B BARREL / CELLULOSE DEGRADATION | |||||||||
Function / homology | Function and homology information cellulose 1,4-beta-cellobiosidase (non-reducing end) / cellulose 1,4-beta-cellobiosidase activity / polysaccharide binding / endo-1,4-beta-xylanase activity / endo-1,4-beta-xylanase / xylan catabolic process / cellulose catabolic process Similarity search - Function | |||||||||
Biological species | Cellulomonas fimi (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / MOLECULAR SUBSTITUTION / Resolution: 1.9 Å | |||||||||
Authors | Monem, V. / Birsan, C. / Warren, R.A.J. / Withers, S.G. / Rose, D.R. | |||||||||
Citation | Journal: Biochemistry / Year: 1998 Title: Exploring the cellulose/xylan specificity of the beta-1,4-glycanase cex from Cellulomonas fimi through crystallography and mutation. Authors: Notenboom, V. / Birsan, C. / Warren, R.A. / Withers, S.G. / Rose, D.R. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2xyl.cif.gz | 71.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2xyl.ent.gz | 55.2 KB | Display | PDB format |
PDBx/mmJSON format | 2xyl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xy/2xyl ftp://data.pdbj.org/pub/pdb/validation_reports/xy/2xyl | HTTPS FTP |
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-Related structure data
Related structure data | 2exoS 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: 34051.941 Da / Num. of mol.: 1 / Fragment: CATALYTIC DOMAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) Cellulomonas fimi (bacteria) / Production host: Escherichia coli (E. coli) References: GenBank: 144429, UniProt: P07986*PLUS, cellulose 1,4-beta-cellobiosidase (non-reducing end) |
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#2: Polysaccharide | beta-D-xylopyranose-(1-4)-2-deoxy-2-fluoro-alpha-D-xylopyranose Source method: isolated from a genetically manipulated source |
#3: 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: 2.32 Å3/Da / Density % sol: 46.97 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 4.6 Details: 7-10% PEG 4K, .1M NAACETATE PH4.6 60 MG/ML PROTEIN CONCENTRATION SOAK 48 HRS WITH 2F-XYLOBIOSE-DNP | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop / Details: Bedarkar, S., (1992) J.Mol. Biol, 228, 693. | ||||||||||||||||||||||||||||||||||||
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 RUH2R / Wavelength: 1.5418 |
Detector | Type: XUONG-HAMLIN MULTIWIRE / Detector: AREA DETECTOR / Date: Apr 1, 1996 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Highest resolution: 1.9 Å / Num. obs: 25857 / % possible obs: 99.94 % / Observed criterion σ(I): 2 / Redundancy: 7.64 % / Rsym value: 0.0803 / Net I/σ(I): 16.19 |
Reflection shell | Resolution: 1.9→2.05 Å / Redundancy: 5.06 % / Mean I/σ(I) obs: 3.58 / Rsym value: 0.2703 / % possible all: 99.9 |
Reflection | *PLUS Num. measured all: 197626 / Rmerge(I) obs: 0.0803 |
Reflection shell | *PLUS Highest resolution: 1.9 Å / % possible obs: 99.9 % / Num. unique obs: 5050 / Num. measured obs: 25539 / Rmerge(I) obs: 0.2703 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR SUBSTITUTION Starting model: PDB ENTRY 2EXO Resolution: 1.9→10 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.0001 / Cross valid method: THROUGHOUT / σ(F): 2
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Displacement parameters | Biso mean: 13 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→10 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.99 Å / Rfactor Rfree error: 0.023 / Total num. of bins used: 8
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.851 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor Rfree: 0.26 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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