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- PDB-5mch: Radiation damage to GH7 Family Cellobiohydrolase from Daphnia pul... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5mch | |||||||||
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Title | Radiation damage to GH7 Family Cellobiohydrolase from Daphnia pulex: Dose (DWD) 9.75 MGy | |||||||||
![]() | Cellobiohydrolase CHBI | |||||||||
![]() | HYDROLASE / Glycoside hydrolase / Cellobiohydrolase / radiation damage | |||||||||
Function / homology | ![]() cellulose 1,4-beta-cellobiosidase (non-reducing end) / cellulose 1,4-beta-cellobiosidase activity / cellulose catabolic process Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() ![]() | |||||||||
![]() | Bury, C.S. / McGeehan, J.E. / Ebrahim, A. / Garman, E.F. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: OH cleavage from tyrosine: debunking a myth. Authors: Bury, C.S. / Carmichael, I. / Garman, E.F. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 191.7 KB | Display | ![]() |
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PDB format | ![]() | 149.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 451.3 KB | Display | ![]() |
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Full document | ![]() | 452.2 KB | Display | |
Data in XML | ![]() | 37.2 KB | Display | |
Data in CIF | ![]() | 55.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5mccC ![]() 5mcdC ![]() 5mceC ![]() 5mcfC ![]() 5mciC ![]() 5mcjC ![]() 5mckC ![]() 5mclC ![]() 5mcmC ![]() 5mcnC ![]() 4xnnS 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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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 48230.168 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: E9G5J5, cellulose 1,4-beta-cellobiosidase (non-reducing end) #2: Chemical | #3: Chemical | ChemComp-SO4 / | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.55 Å3/Da / Density % sol: 51.7 % / Mosaicity: 0 ° |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 4 / Details: 900mM ammonium sulphate, 100mM monosodium citrate |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Feb 29, 2016 | ||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 | ||||||||||||||||||
Reflection | Resolution: 2→82.57 Å / Num. obs: 66183 / % possible obs: 99.8 % / Redundancy: 3.3 % / Biso Wilson estimate: 32.76 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.077 / Rpim(I) all: 0.05 / Rrim(I) all: 0.092 / Net I/σ(I): 8.3 / Num. measured all: 215589 / Scaling rejects: 271 | ||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: ![]() |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: pdbid 4XNN Resolution: 2→82.568 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.86
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 90.31 Å2 / Biso mean: 37.7742 Å2 / Biso min: 18.4 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2→82.568 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 23
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