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- PDB-2yoy: Bacillus amyloliquefaciens CBM33 in complex with Cu(I) reduced us... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2yoy | ||||||
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Title | Bacillus amyloliquefaciens CBM33 in complex with Cu(I) reduced using ascorbate | ||||||
![]() | RBAM17540 | ||||||
![]() | OXIDOREDUCTASE / CELLULOSE OXIDATION / GH61 / CELLULOSE DEGRADATION | ||||||
Function / homology | chitin-binding protein cbp21 / Coagulation Factor XIII; Chain A, domain 1 / Distorted Sandwich / Mainly Beta / COPPER (I) ION / : ![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Hemsworth, G.R. / Taylor, E.J. / Kim, R.Q. / Lewis, S.J. / Turkenburg, J.P. / Davies, G.J. / Walton, P.H. | ||||||
![]() | ![]() Title: The Copper Active Site of Cbm33 Polysaccharide Oxygenases. Authors: Hemsworth, G.R. / Taylor, E.J. / Kim, R.Q. / Gregory, R.C. / Lewis, S.J. / Turkenburg, J.P. / Parkin, A. / Davies, G.J. / Walton, P.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 | ![]() | 89.1 KB | Display | ![]() |
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PDB format | ![]() | 67.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 441.3 KB | Display | ![]() |
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Full document | ![]() | 441.5 KB | Display | |
Data in XML | ![]() | 17.9 KB | Display | |
Data in CIF | ![]() | 26 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related 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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: HIS / Beg label comp-ID: HIS / End auth comp-ID: THR / End label comp-ID: THR / Refine code: _ / Auth seq-ID: 28 - 205 / Label seq-ID: 1 - 178
NCS oper: (Code: given Matrix: (0.99997, 0.0077, -0.00302), Vector: |
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Components
#1: Protein | Mass: 19717.844 Da / Num. of mol.: 2 / Fragment: RESIDUES 28-205 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | #3: Chemical | ChemComp-EDO / #4: Water | ChemComp-HOH / | Sequence details | LEADER PEPTIDE WAS NOT INCLUDED IN THE CONSTRUCT BUT REPLACED BY PELB LEADER TO DIRECT PROTEIN TO PERIPLASM | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.39 Å3/Da / Density % sol: 48 % / Description: NONE |
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Crystal grow | pH: 4 / Details: 0.1M MMT BUFFER PH 4.0, 25% PEG-1500 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 16, 2012 / Details: MIRRORS |
Radiation | Monochromator: SINGLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.976 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→41.6 Å / Num. obs: 42480 / % possible obs: 99.9 % / Observed criterion σ(I): 6 / Redundancy: 6.2 % / Rmerge(I) obs: 0.14 / Net I/σ(I): 8.2 |
Reflection shell | Resolution: 1.7→1.79 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.82 / Mean I/σ(I) obs: 2.6 / % possible all: 99.9 |
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Processing
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Refinement | Method to determine structure: OTHER Starting model: NONE Resolution: 1.7→41.64 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.938 / SU B: 2.461 / SU ML: 0.081 / Cross valid method: THROUGHOUT / ESU R: 0.121 / ESU R Free: 0.119 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
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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: SIMPLE MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.829 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→41.64 Å
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Refine LS restraints |
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