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Yorodumi- PDB-1oc7: D405N mutant of the CELLOBIOHYDROLASE CEL6A FROM HUMICOLA INSOLEN... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1oc7 | |||||||||
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Title | D405N mutant of the CELLOBIOHYDROLASE CEL6A FROM HUMICOLA INSOLENS in complex with methyl-tetrathio-alpha-d-cellopentoside at 1.1 angstrom resolution | |||||||||
Components | CELLOBIOHYDROLASE II | |||||||||
Keywords | HYDROLASE / CELLULOSE DEGRADATION / CELLOBIOHYDROLASE / CELLULASE / GLYCOSIDE HYDROLASE FAMILY 6 / PROCESSIVE MECHANISM | |||||||||
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 | HUMICOLA INSOLENS (fungus) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.11 Å | |||||||||
Authors | Varrot, A. / Frandsen, T.P. / Von Ossowski, I. / Boyer, V. / Driguez, H. / Schulein, M. / Davies, G.J. | |||||||||
Citation | Journal: Structure / Year: 2003 Title: Structural Basis for Ligand Binding and Processivity in Cellobiohydrolase Cel6A from Humicola Insolens Authors: Varrot, A. / Frandsen, T.P. / Von Ossowski, I. / Boyer, V. / Driguez, H. / Schulein, M. / 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 | 1oc7.cif.gz | 186.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1oc7.ent.gz | 144.4 KB | Display | PDB format |
PDBx/mmJSON format | 1oc7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1oc7_validation.pdf.gz | 735.6 KB | Display | wwPDB validaton report |
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Full document | 1oc7_full_validation.pdf.gz | 739.8 KB | Display | |
Data in XML | 1oc7_validation.xml.gz | 22.6 KB | Display | |
Data in CIF | 1oc7_validation.cif.gz | 35.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oc/1oc7 ftp://data.pdbj.org/pub/pdb/validation_reports/oc/1oc7 | HTTPS FTP |
-Related structure data
Related structure data | 1oc5SC 1oc6C 1ocbC 1ocjC 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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Unit cell |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 40181.723 Da / Num. of mol.: 1 / Fragment: CATALYTIC CORE DOMAIN RESIDUES 87-450 / Mutation: YES Source method: isolated from a genetically manipulated source Details: N-LINKED N-ACETYLGLUCOSAMINE ON RESIDUE ASN 141 / Source: (gene. exp.) HUMICOLA INSOLENS (fungus) Plasmid: UNDER CONTROL OF THE FUNGAL AMYLASE PROMOTER AND AMYLOGLUCOSIDASE TERMINATOR Production host: ASPERGILLUS ORYZAE (mold) References: UniProt: Q9C1S9*PLUS, cellulose 1,4-beta-cellobiosidase (non-reducing end) |
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-Sugars , 2 types, 2 molecules
#2: Polysaccharide | beta-D-glucopyranose-(1-4)-4-thio-beta-D-glucopyranose-(1-4)-4-thio-beta-D-glucopyranose-(1-4)-4- ...beta-D-glucopyranose-(1-4)-4-thio-beta-D-glucopyranose-(1-4)-4-thio-beta-D-glucopyranose-(1-4)-4-thio-beta-D-glucopyranose-(1-4)-methyl 4-thio-alpha-D-glucopyranoside Type: oligosaccharide / Mass: 907.006 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source |
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#3: Sugar | ChemComp-NAG / |
-Non-polymers , 5 types, 609 molecules
#4: Chemical | ChemComp-MG / | ||||
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#5: Chemical | ChemComp-ACT / | ||||
#6: Chemical | #7: Chemical | #8: Water | ChemComp-HOH / | |
-Details
Compound details | ENGINEEREDSequence details | THIS MUTANT HAS BEEN PRODUCED BY SITE DIRECTED MUTAGENESIS. THE CLONING WAS PERFORMED SUCH AS ONLY ...THIS MUTANT HAS BEEN PRODUCED BY SITE DIRECTED MUTAGENESI | |
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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: 4.05 Å3/Da / Density % sol: 38.8 % | ||||||||||||||||||||||||
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Crystal grow | pH: 4.6 Details: PROTEIN WAS CONCENTRATED TO 20 MG/ML IN WATER. CRYSTALLISATION IN 100MM MAGNESIUM ACETATE, 100MM ACETATE BUFFER AT PH 4.6. PRECIPITANT WAS 21% POLYETHYLENE GLYCOL 5000MME AND 5% ...Details: PROTEIN WAS CONCENTRATED TO 20 MG/ML IN WATER. CRYSTALLISATION IN 100MM MAGNESIUM ACETATE, 100MM ACETATE BUFFER AT PH 4.6. PRECIPITANT WAS 21% POLYETHYLENE GLYCOL 5000MME AND 5% DIMETHYLFORMAMIDE AS ADDITIVE.THE PROTEIN WAS INCUBATED WITH 1MM OF THE INHIBITOR PRIOR CRYSTALLISATION FOR AT LEAST 1 HOUR. | ||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||
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: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.8445 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 15, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8445 Å / Relative weight: 1 |
Reflection | Resolution: 1.1→20 Å / Num. obs: 120133 / % possible obs: 96 % / Observed criterion σ(I): 0 / Redundancy: 4.3 % / Rmerge(I) obs: 0.053 / Net I/σ(I): 23.7 |
Reflection shell | Resolution: 1.1→1.13 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.242 / Mean I/σ(I) obs: 5.6 / % possible all: 91.5 |
Reflection | *PLUS Highest resolution: 1.1 Å / Lowest resolution: 20 Å / % possible obs: 95 % / Redundancy: 4.3 % / Rmerge(I) obs: 0.053 |
Reflection shell | *PLUS Highest resolution: 1.1 Å / % possible obs: 91.5 % / Redundancy: 4.3 % / Rmerge(I) obs: 0.242 / Mean I/σ(I) obs: 5.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1OC5 Resolution: 1.11→20 Å / Cor.coef. Fo:Fc: 0.984 / Cor.coef. Fo:Fc free: 0.98 / SU B: 0.286 / SU ML: 0.014 / Cross valid method: THROUGHOUT / ESU R: 0.024 / ESU R Free: 0.025 / 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: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 8.57 Å2
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Refinement step | Cycle: LAST / Resolution: 1.11→20 Å
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Refine LS restraints |
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