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Yorodumi- PDB-2his: CELLULOMONAS FIMI XYLANASE/CELLULASE DOUBLE MUTANT E127A/H205N WI... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2his | |||||||||
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Title | CELLULOMONAS FIMI XYLANASE/CELLULASE DOUBLE MUTANT E127A/H205N WITH COVALENT CELLOBIOSE | |||||||||
Components | CELLULOMONAS FIMI FAMILY 10 BETA-1,4-GLYCANASE | |||||||||
Keywords | HYDROLASE / O-GLYCOSYL / XYLANASE/CELLULASE / A/B BARREL | |||||||||
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: 1.84 Å | |||||||||
Authors | Notenboom, V. / Birsan, C. / Nitz, M. / Rose, D.R. / Warren, R.A.J. / Wither, S.G. | |||||||||
Citation | Journal: Nat.Struct.Biol. / Year: 1998 Title: Insights into transition state stabilization of the beta-1,4-glycosidase Cex by covalent intermediate accumulation in active site mutants. Authors: Notenboom, V. / Birsan, C. / Nitz, M. / Rose, D.R. / Warren, R.A. / Withers, S.G. #1: Journal: Biochemistry / Year: 1994 Title: Crystal Structure of the Catalytic Domain of the Beta-1,4-Glycanase Cex from Cellulomonas Fimi Authors: White, A. / Withers, S.G. / Gilkes, N.R. / Rose, D.R. #2: Journal: J.Mol.Biol. / Year: 1992 Title: Crystallization and Preliminary X-Ray Diffraction Analysis of the Catalytic Domain of Cex, an Exo-Beta-1,4-Glucanase and Beta-1,4-Xylanase from the Bacterium Cellulomonas Fimi Authors: Bedarkar, S. / Gilkes, N.R. / Kilburn, D.G. / Kwan, E. / Rose, D.R. / Miller Junior, R.C. / Warren, R.A. / Withers, S.G. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2his.cif.gz | 72.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2his.ent.gz | 55.9 KB | Display | PDB format |
PDBx/mmJSON format | 2his.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hi/2his ftp://data.pdbj.org/pub/pdb/validation_reports/hi/2his | 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 33969.859 Da / Num. of mol.: 1 / Fragment: CATALYTIC DOMAIN / Mutation: E127A, H205N Source method: isolated from a genetically manipulated source Details: COVALENT INTERMEDIATE / Source: (gene. exp.) Cellulomonas fimi (bacteria) / Production host: Escherichia coli (E. coli) References: UniProt: P07986, cellulose 1,4-beta-cellobiosidase (non-reducing end) |
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#2: Polysaccharide | beta-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-cellobiose |
#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: 46.98 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 4.6 Details: 15-20% PEG 4K,.1M NAACETATE PH4.6 45 MG/ML PROTEIN CONCENTRATION PRE-COMPLEXED WITH CELLOBIOSE-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: Jan 1, 1997 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Highest resolution: 1.74 Å / Num. obs: 32211 / % possible obs: 96.1 % / Observed criterion σ(I): 2 / Redundancy: 4.7 % / Rsym value: 0.0681 / Net I/σ(I): 16.19 |
Reflection shell | Resolution: 1.74→1.81 Å / Redundancy: 4.41 % / Mean I/σ(I) obs: 2.01 / Rsym value: 0.3611 / % possible all: 80.4 |
Reflection | *PLUS Num. measured all: 255846 / Rmerge(I) obs: 0.0681 |
Reflection shell | *PLUS % possible obs: 80.4 % / Num. unique obs: 5297 / Num. measured obs: 23362 / Rmerge(I) obs: 0.3611 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR SUBSTITUTION Starting model: PDB ENTRY 2EXO Resolution: 1.84→15 Å / Rfactor Rfree error: 0.0059 / 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: 21.14 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.84→15 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.84→1.92 Å / Rfactor Rfree error: 0.021 / 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 Num. reflection obs: 30163 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.32 |