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Yorodumi- PDB-4ax6: HYPOCREA JECORINA CEL6A D221A MUTANT SOAKED WITH 6-CHLORO-4- PHEN... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4ax6 | |||||||||
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Title | HYPOCREA JECORINA CEL6A D221A MUTANT SOAKED WITH 6-CHLORO-4- PHENYLUMBELLIFERYL-BETA-CELLOBIOSIDE | |||||||||
Components | EXOGLUCANASE 2Cellulose 1,4-beta-cellobiosidase | |||||||||
Keywords | HYDROLASE / HYDROLASE(O-GLYCOSYL) / GLYCOSIDASE / GLYCOSIDE HYDROLASE / GH6 / CLPHUFG2 / CELLULASE / CELLOBIOHYDROLASE / GLYCOPROTEIN / FLUOROGENIC SUBSTRATE | |||||||||
Function / homology | Function and homology information cellulose 1,4-beta-cellobiosidase (non-reducing end) / cellulose 1,4-beta-cellobiosidase activity / cellulose binding / cellulose catabolic process / extracellular region / identical protein binding Similarity search - Function | |||||||||
Biological species | TRICHODERMA REESEI (fungus) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | |||||||||
Authors | Wu, M. / Nerinckx, W. / Piens, K. / Ishida, T. / Hansson, H. / Stahlberg, J. / Sandgren, M. | |||||||||
Citation | Journal: FEBS J. / Year: 2013 Title: Rational Design, Synthesis, Evaluation and Enzyme-Substrate Structures of Improved Fluorogenic Substrates for Family 6 Glycoside Hydrolases. Authors: Wu, M. / Nerinckx, W. / Piens, K. / Ishida, T. / Hansson, H. / Sandgren, M. / Stahlberg, J. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4ax6.cif.gz | 163 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ax6.ent.gz | 127 KB | Display | PDB format |
PDBx/mmJSON format | 4ax6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ax/4ax6 ftp://data.pdbj.org/pub/pdb/validation_reports/ax/4ax6 | HTTPS FTP |
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-Related structure data
Related structure data | 4au0C 4ax7C 1hgyS 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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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 38867.152 Da / Num. of mol.: 2 / Fragment: CATALYTIC DOMAIN, RESIDUES 109-471 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) TRICHODERMA REESEI (fungus) / Production host: TRICHODERMA REESEI (fungus) References: UniProt: P07987, cellulose 1,4-beta-cellobiosidase (non-reducing end) |
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-Sugars , 3 types, 18 molecules
#2: Polysaccharide | #3: Sugar | ChemComp-NAG / #4: Sugar | ChemComp-MAN / |
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-Non-polymers , 2 types, 546 molecules
#5: Chemical | #6: Water | ChemComp-HOH / | |
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-Details
Compound details | 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: 2.1 Å3/Da / Density % sol: 41.5 % / Description: NONE |
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Crystal grow | pH: 6 Details: 20% PEG 5000 MONOMETHYL ETHER (FLUKA) AND 20 MM SODIUM MES BUFFER, PH 6.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.933 |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→35.7 Å / Num. obs: 31621 / % possible obs: 98.3 % / Observed criterion σ(I): 2 / Redundancy: 3.8 % / Rmerge(I) obs: 0.2 / Net I/σ(I): 6.7 |
Reflection shell | Resolution: 2.2→2.3 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 3.2 / % possible all: 97.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1HGY Resolution: 2.3→64.17 Å / Cor.coef. Fo:Fc: 0.908 / Cor.coef. Fo:Fc free: 0.857 / SU B: 9.264 / SU ML: 0.219 / Cross valid method: THROUGHOUT / ESU R: 1.205 / ESU R Free: 0.294 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 13.195 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→64.17 Å
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Refine LS restraints |
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