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- PDB-1oc5: D405N mutant of the CELLOBIOHYDROLASE CEL6A FROM HUMICOLA INSOLEN... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1oc5 | |||||||||
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Title | D405N mutant of the CELLOBIOHYDROLASE CEL6A FROM HUMICOLA INSOLENS in complex with methyl-cellobiosyl-4-deoxy-4-thio-beta-D-cellobioside | |||||||||
![]() | CELLOBIOHYDROLASE II | |||||||||
![]() | HYDROLASE / CELLULOSE DEGRADATION / CELLOBIOHYDROLASE / CELLULASE / GLYCOSIDE HYDROLASE FAMILY 6 / PROCESSIVE MECHANISM | |||||||||
Function / homology | ![]() 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 | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Varrot, A. / Frandsen, T.P. / Von Ossowski, I. / Boyer, V. / Driguez, H. / Schulein, M. / Davies, G.J. | |||||||||
![]() | ![]() 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. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 101.4 KB | Display | ![]() |
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PDB format | ![]() | 75 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 705.7 KB | Display | ![]() |
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Full document | ![]() | 707.4 KB | Display | |
Data in XML | ![]() | 20.7 KB | Display | |
Data in CIF | ![]() | 32.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1oc6C ![]() 1oc7C ![]() 1ocbC ![]() 1ocjC ![]() 1bvwS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#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.) ![]() Plasmid: UNDER CONTROL OF THE FUNGAL AMYLASE PROMOTER AND AMYLOGLUCOSIDASE TERMINATOR Production host: ![]() ![]() References: UniProt: Q9C1S9*PLUS, cellulose 1,4-beta-cellobiosidase (non-reducing end) | ||||||
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#2: Polysaccharide | beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-4-thio-beta-D-glucopyranose-(1-4)-methyl beta- ...beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-4-thio-beta-D-glucopyranose-(1-4)-methyl beta-D-glucopyranoside Type: oligosaccharide / Mass: 696.669 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source | ||||||
#3: Sugar | ChemComp-NAG / | ||||||
#4: Chemical | ChemComp-GOL / #5: Water | ChemComp-HOH / | Compound details | ENGINEERED | Sequence 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 | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.05 Å3/Da / Density % sol: 38.8 % Description: NATIVE WILD-TYPE STRUCTURE OF CEL6A FROM HUMICOLA INSOLENS | ||||||||||||||||||||||||
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Crystal grow | pH: 7.5 Details: PROTEIN WAS CONCENTRATED TO 20 MG/ML IN WATER. CRYSTALLISATION IN 100MM MAGNESIUM ACETATE IN 100MM HEPES BUFFER AT PH 7.5. PRECIPITANT WAS 16% POLYETHYLENE GLYCOL 5000MME. THE PROTEIN WAS ...Details: PROTEIN WAS CONCENTRATED TO 20 MG/ML IN WATER. CRYSTALLISATION IN 100MM MAGNESIUM ACETATE IN 100MM HEPES BUFFER AT PH 7.5. PRECIPITANT WAS 16% POLYETHYLENE GLYCOL 5000MME. THE PROTEIN WAS INCUBATED WITH 1MM OF THE INHIBITOR PRIOR CRYSTALLISATION. | ||||||||||||||||||||||||
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: ![]() ![]() ![]() |
Detector | Type: ADSC CCD / Detector: CCD / Date: Sep 15, 1999 / Details: TOROIDAL MIRROR |
Radiation | Monochromator: SILICON / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9393 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→50 Å / Num. obs: 33830 / % possible obs: 93.9 % / Observed criterion σ(I): 0 / Redundancy: 2.9 % / Rmerge(I) obs: 0.055 / Net I/σ(I): 17 |
Reflection shell | Resolution: 1.7→1.76 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.157 / Mean I/σ(I) obs: 5.8 / % possible all: 88.7 |
Reflection | *PLUS Highest resolution: 1.7 Å / Lowest resolution: 50 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.055 |
Reflection shell | *PLUS % possible obs: 88.7 % / Redundancy: 2.7 % / Rmerge(I) obs: 0.157 / Mean I/σ(I) obs: 5.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1BVW Resolution: 1.7→50 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.951 / SU B: 1.609 / SU ML: 0.054 / Cross valid method: THROUGHOUT / ESU R: 0.094 / ESU R Free: 0.095 / 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: 9.09 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→50 Å
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Refine LS restraints |
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