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- PDB-4d5o: Hypocrea jecorina cellobiohydrolase Cel7A E212Q soaked with xylop... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4d5o | |||||||||||||||
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Title | Hypocrea jecorina cellobiohydrolase Cel7A E212Q soaked with xylopentaose. | |||||||||||||||
![]() | CELLULOSE 1,4-BETA-CELLOBIOSIDASE | |||||||||||||||
![]() | HYDROLASE / GLYCOSIDE HYDROLASE / CELLOBIOHYDROLASE / CELLULASE. INHIBITION / XYLOOLIGOSACCHARIDES | |||||||||||||||
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 | ![]() ![]() ![]() | |||||||||||||||
![]() | Momeni, M.H. / Ubhayasekera, W. / Stahlberg, J. / Hansson, H. | |||||||||||||||
![]() | ![]() Title: Structural Insights Into the Inhibition of Cellobiohydrolase Cel7A by Xylooligosaccharides. Authors: Haddad Momeni, M. / Ubhayasekera, W. / Sandgren, M. / Stahlberg, J. / Hansson, H. | |||||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 115 KB | Display | ![]() |
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PDB format | ![]() | 86.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 984.7 KB | Display | ![]() |
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Full document | ![]() | 986.6 KB | Display | |
Data in XML | ![]() | 24 KB | Display | |
Data in CIF | ![]() | 37.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4d5iC ![]() 4d5jC ![]() 4d5pC ![]() 4d5qC ![]() 4d5vC ![]() 3celS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 46067.754 Da / Num. of mol.: 1 / Fragment: CATALYTIC MODULE, RESIDUES 18-451 / Mutation: YES Source method: isolated from a genetically manipulated source Details: COMPLEX WITH XYLOTETRAOSE LIGAND BOUND AT SUBSITES -7 TO -3 IN THE SUBSTRATE BINDING TUNNEL OF THE ENZYME Source: (gene. exp.) ![]() Description: HYPOCREA JECORINA WAS PREVIOUSLY KNOWN AS TRICHODERMA REESEI. Variant: VTT-D-93201 / Plasmid: PEM-F5 / Production host: ![]() References: UniProt: P62694, cellulose 1,4-beta-cellobiosidase (reducing end) |
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-Sugars , 3 types, 3 molecules ![](data/chem/img/NAG.gif)
#2: Polysaccharide | beta-D-xylopyranose-(1-4)-beta-D-xylopyranose-(1-4)-beta-D-xylopyranose-(1-4)-beta-D-xylopyranose Source method: isolated from a genetically manipulated source |
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#3: Polysaccharide | beta-D-galactopyranose-(1-4)-beta-D-glucopyranose / beta-lactose |
#5: Sugar | ChemComp-NAG / |
-Non-polymers , 3 types, 564 molecules ![](data/chem/img/CO.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | #6: Chemical | ChemComp-GOL / | #7: Water | ChemComp-HOH / | |
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-Details
Nonpolymer details | COBALT (II) ION (CO): 10 MM COBALT CHLORIDE WAS PRESENT IN CRYSTALLISATION SOLUTION PYROGLUTAMIC ...COBALT (II) ION (CO): 10 MM COBALT CHLORIDE WAS PRESENT IN CRYSTALLIS |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.07 Å3/Da / Density % sol: 40.6 % / Description: NONE |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 0.1 M NA-MES (PH 6.0), 20% MONOMETHYL ETHER PEG 5000, 0.01 M COCL2, 12.5% GLYCEROL, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH MAR165 / Detector: CCD / Date: Oct 19, 2010 / Details: MIRRORS |
Radiation | Monochromator: BENT SI (111) CRYSTAL, HORIZONTALLY FOCUSING / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.041 Å / Relative weight: 1 |
Reflection | Resolution: 1.52→27.52 Å / Num. obs: 57623 / % possible obs: 98.2 % / Observed criterion σ(I): 2 / Redundancy: 6.7 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 17.1 |
Reflection shell | Resolution: 1.52→1.6 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 5.1 / % possible all: 87.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 3CEL Resolution: 1.52→66.39 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.921 / SU B: 2.023 / SU ML: 0.073 / Cross valid method: THROUGHOUT / ESU R: 0.106 / ESU R Free: 0.105 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT. U VALUES, REFINED INDIVIDUALLY A XYLOTETRAOSE LIGAND AT SUBSITES -7 TO -3 IN THE ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT. U VALUES, REFINED INDIVIDUALLY A XYLOTETRAOSE LIGAND AT SUBSITES -7 TO -3 IN THE SUBSTRATE BINDING TUNNEL OF THE ENZYME IS INCLUDED IN THE FINAL MODEL.
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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: 15.351 Å2
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Refinement step | Cycle: LAST / Resolution: 1.52→66.39 Å
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Refine LS restraints |
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