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Yorodumi- PDB-5oa5: CELLOBIOHYDROLASE I (CEL7A) FROM HYPOCREA JECORINA WITH IMPROVED ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5oa5 | |||||||||
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Title | CELLOBIOHYDROLASE I (CEL7A) FROM HYPOCREA JECORINA WITH IMPROVED THERMAL STABILITY | |||||||||
Components | Exoglucanase 1Cellulose 1,4-beta-cellobiosidase | |||||||||
Keywords | HYDROLASE / CELLULASE / PROTEIN ENGINEERING | |||||||||
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 Similarity search - Function | |||||||||
Biological species | Hypocrea jecorina (fungus) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | |||||||||
Authors | Goedegebuur, F. / Hansson, H. / Karkehabadi, S. / Mikkelsen, N. / Stahlberg, J. / Sandgren, M. | |||||||||
Funding support | United States, 2items
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Citation | Journal: J. Biol. Chem. / Year: 2017 Title: Improving the thermal stability of cellobiohydrolase Cel7A from Hypocrea jecorina by directed evolution. Authors: Goedegebuur, F. / Dankmeyer, L. / Gualfetti, P. / Karkehabadi, S. / Hansson, H. / Jana, S. / Huynh, V. / Kelemen, B.R. / Kruithof, P. / Larenas, E.A. / Teunissen, P.J.M. / Stahlberg, J. / ...Authors: Goedegebuur, F. / Dankmeyer, L. / Gualfetti, P. / Karkehabadi, S. / Hansson, H. / Jana, S. / Huynh, V. / Kelemen, B.R. / Kruithof, P. / Larenas, E.A. / Teunissen, P.J.M. / Stahlberg, J. / Payne, C.M. / Mitchinson, C. / Sandgren, M. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5oa5.cif.gz | 186.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5oa5.ent.gz | 146.1 KB | Display | PDB format |
PDBx/mmJSON format | 5oa5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oa/5oa5 ftp://data.pdbj.org/pub/pdb/validation_reports/oa/5oa5 | HTTPS FTP |
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-Related structure data
Related structure data | 2v3iS 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 46262.238 Da / Num. of mol.: 2 / Fragment: CATALYTIC DOMAIN, RESIDUES 18-451 Mutation: S8P, T41I, N49S, A68T, N89D, S92T, S113N, S196T, P227L, D249K, T255P, S278P, E295K, T296P, T332Y, V304D, S411F Source method: isolated from a genetically manipulated source Source: (gene. exp.) Hypocrea jecorina (fungus) / Gene: cbh1 / Plasmid: pRAXDES / Production host: Aspergillus awamori (mold) / Variant (production host): AP4 References: UniProt: P62694, cellulose 1,4-beta-cellobiosidase (non-reducing end) #2: Sugar | ChemComp-NAG / #3: Chemical | ChemComp-GOL / | #4: Water | ChemComp-HOH / | Sequence 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: 2.48 Å3/Da / Density % sol: 50.45 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6 Details: 25.5% POLYETHYLENE GLYCOL (PEG) 4000, 0.17 M AMSO4 AND 15% GLYCEROL |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Oct 5, 2012 / Details: PT COATED MIRRORS |
Radiation | Monochromator: HORIZONTALLY DIFFRACTING SI (111) MONOCHROMATOR Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8726 Å / Relative weight: 1 |
Reflection | Resolution: 1.99→41.16 Å / Num. obs: 56990 / % possible obs: 99.6 % / Observed criterion σ(I): 2 / Redundancy: 3.71 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 4.9 |
Reflection shell | Resolution: 2.1→2.21 Å / Redundancy: 3.73 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 1.86 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2V3I Resolution: 2.1→41.16 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.926 / SU B: 4.952 / SU ML: 0.13 / Cross valid method: THROUGHOUT / ESU R: 0.226 / ESU R Free: 0.19 / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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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: 17.9 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→41.16 Å
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Refine LS restraints |
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