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Yorodumi- PDB-1ojk: Anatomy of glycosynthesis: Structure and kinetics of the Humicola... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ojk | ||||||||||||
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Title | Anatomy of glycosynthesis: Structure and kinetics of the Humicola insolens Cel7BE197A and E197S glycosynthase mutants | ||||||||||||
Components | ENDOGLUCANASE ICellulase | ||||||||||||
Keywords | HYDROLASE / CELLULOSE DEGRADATION / GLYCOSYNTHASE | ||||||||||||
Function / homology | Function and homology information cellulase / cellulase activity / cellulose catabolic process / extracellular region Similarity search - Function | ||||||||||||
Biological species | HUMICOLA INSOLENS (fungus) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å | ||||||||||||
Authors | Ducros, V.M.-A. / Tarling, C.A. / Zechel, D.L. / Brzozowski, A.M. / Frandsen, T.P. / Von Ossowski, I. / Schulein, M. / Withers, S.G. / Davies, G.J. | ||||||||||||
Citation | Journal: Chem.Biol. / Year: 2003 Title: Anatomy of Glycosynthesis: Structure and Kinetics of the Humicola Insolens Cel7B E197A and E197S Glycosynthase Mutants Authors: Ducros, V.M.-A. / Tarling, C.A. / Zechel, D.L. / Brzozowski, A.M. / Frandsen, T.P. / Von Ossowski, I. / Schulein, M. / Withers, S.G. / Davies, G.J. | ||||||||||||
History |
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Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ojk.cif.gz | 345 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ojk.ent.gz | 280.1 KB | Display | PDB format |
PDBx/mmJSON format | 1ojk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oj/1ojk ftp://data.pdbj.org/pub/pdb/validation_reports/oj/1ojk | HTTPS FTP |
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-Related structure data
Related structure data | 1ojiC 1ojjC 1dymS S: Starting model for refinement C: citing same article (ref.) |
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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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (0.99944, -0.03232, -0.00828), Vector: |
-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 44568.109 Da / Num. of mol.: 2 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) HUMICOLA INSOLENS (fungus) / Production host: ASPERGILLUS ORYZAE (mold) / References: UniProt: P56680, cellulase |
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-Sugars , 3 types, 6 molecules
#2: Polysaccharide | #3: Polysaccharide | #4: Sugar | |
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-Non-polymers , 2 types, 795 molecules
#5: Chemical | #6: Water | ChemComp-HOH / | |
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-Details
Compound details | ENGINEERED RESIDUE GLU 197 SER N-LINKED N-ACETYLGLUCOSAMINE ON RESIDUE ASN 247, PYROGLUTAMATE POST- ...ENGINEERED |
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Sequence details | PYROGLUTAM |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 47.7 % | ||||||||||||||||||||||||
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 7 Details: HANGING DROPS 20MM TRIS-HCL PH7-8.5, 15-30% POLYETHYLENE GLYCOL 4000, pH 7.00 | ||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop / PH range low: 8.5 / PH range high: 7 | ||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 |
Detector | Type: MARRESEARCH / Detector: CCD / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.934 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→30 Å / Num. obs: 129121 / % possible obs: 99.3 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.043 / Net I/σ(I): 24 |
Reflection shell | Resolution: 1.5→1.55 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 3.8 / % possible all: 97.4 |
Reflection | *PLUS Highest resolution: 1.5 Å / Lowest resolution: 30 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.043 |
Reflection shell | *PLUS Highest resolution: 1.5 Å / % possible obs: 97.4 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 3.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1DYM Resolution: 1.5→29.88 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.957 / SU B: 2.039 / SU ML: 0.035 / Cross valid method: THROUGHOUT / ESU R: 0.076 / ESU R Free: 0.064 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 11.91 Å2
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Refinement step | Cycle: LAST / Resolution: 1.5→29.88 Å
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Refine LS restraints |
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