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Yorodumi- PDB-2yok: Cellobiohydrolase I Cel7A from Trichoderma harzianum at 1.7 A res... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2yok | ||||||||||||
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Title | Cellobiohydrolase I Cel7A from Trichoderma harzianum at 1.7 A resolution | ||||||||||||
Components | EXOGLUCANASE 1 | ||||||||||||
Keywords | HYDROLASE / ENZYMATIC HYDROLYSIS / BIOMASS / DEPOLYMERIZATION / CELLULOSIC ETHANOL | ||||||||||||
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 LIXII (fungus) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.67 Å | ||||||||||||
Authors | Textor, L.C. / Colussi, F. / Serpa, V. / Squina, F.M. / Pereira Jr, N. / Polikarpov, I. | ||||||||||||
Citation | Journal: FEBS J. / Year: 2013 Title: Joint X-Ray Crystallographic and Molecular Dynamics Study of Cellobiohydrolase I from Trichoderma Harzianum: Deciphering the Structural Features of Cellobiohydrolase Catalytic Activity. Authors: Textor, L.C. / Colussi, F. / Silveira, R.L. / Serpa, V. / De Mello, B.L. / Muniz, J.R.C. / Squina, F.M. / Pereira, N.J. / Skaf, M.S. / Polikarpov, I. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2yok.cif.gz | 185.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2yok.ent.gz | 144.5 KB | Display | PDB format |
PDBx/mmJSON format | 2yok.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2yok_validation.pdf.gz | 728.7 KB | Display | wwPDB validaton report |
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Full document | 2yok_full_validation.pdf.gz | 731 KB | Display | |
Data in XML | 2yok_validation.xml.gz | 25.2 KB | Display | |
Data in CIF | 2yok_validation.cif.gz | 40.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yo/2yok ftp://data.pdbj.org/pub/pdb/validation_reports/yo/2yok | HTTPS FTP |
-Related structure data
Related structure data | 1celS 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: 45151.016 Da / Num. of mol.: 1 / Fragment: CATALYTIC CORE DOMAIN, RESIDUES 18-443 / Source method: isolated from a natural source Details: COVALENT LINK BETWEEN N 397 AND NAG 903 COVALENT LINK BETWEEN N 126 AND NAG 902 COVALENT LINK BETWEEN N 283 AND NAG 901 COVALENT LINK BETWEEN C 274 AND C 344 COVALENT LINK BETWEEN C 66 AND C ...Details: COVALENT LINK BETWEEN N 397 AND NAG 903 COVALENT LINK BETWEEN N 126 AND NAG 902 COVALENT LINK BETWEEN N 283 AND NAG 901 COVALENT LINK BETWEEN C 274 AND C 344 COVALENT LINK BETWEEN C 66 AND C 87 COVALENT LINK BETWEEN C 77 AND C 83 COVALENT LINK BETWEEN C 189 AND C 222 COVALENT LINK BETWEEN C 251 AND C 256 COVALENT LINK BETWEEN C 21 AND C 88 COVALENT LINK BETWEEN C 36 AND C 41 COVALENT LINK BETWEEN C 151 AND C 410 COVALENT LINK BETWEEN C 185 AND C 223 Source: (natural) HYPOCREA LIXII (fungus) References: UniProt: Q9P8P3, cellulose 1,4-beta-cellobiosidase (non-reducing end) | ||||||
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#2: Sugar | #3: Chemical | ChemComp-PE4 / | #4: Chemical | ChemComp-PEG / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 1.77 Å3/Da / Density % sol: 31 % / Description: NONE |
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Crystal grow | Details: 25% PEG 4000 AND 5 MM CACL2 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1.46 |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.46 Å / Relative weight: 1 |
Reflection | Resolution: 1.67→45.3 Å / Num. obs: 42070 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Redundancy: 6.1 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 24.4 |
-Processing
Software | Name: REFMAC / Version: 5.7.0029 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1CEL Resolution: 1.67→39.48 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.963 / SU B: 2.68 / SU ML: 0.048 / Cross valid method: THROUGHOUT / ESU R: 0.091 / ESU R Free: 0.087 / 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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 12.402 Å2
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Refinement step | Cycle: LAST / Resolution: 1.67→39.48 Å
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