+Open data
-Basic information
Entry | Database: PDB / ID: 7b21 | |||||||||
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Title | The X183 domain from Cellvibrio japonicus Cbp2D | |||||||||
Components | Carbohydrate binding protein, putative, cbp2D | |||||||||
Keywords | ELECTRON TRANSPORT / X183 / c-type cytochrome / Cbp2D / Cellvibrio japonicus | |||||||||
Function / homology | Function and homology information polysaccharide binding / hydrolase activity, hydrolyzing O-glycosyl compounds / electron transfer activity / carbohydrate metabolic process / heme binding / metal ion binding Similarity search - Function | |||||||||
Biological species | Cellvibrio japonicus (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.2 Å | |||||||||
Authors | Branch, J. / Hemsworth, G.R. | |||||||||
Funding support | United Kingdom, 1items
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Citation | Journal: Biochem.J. / Year: 2021 Title: C-type cytochrome-initiated reduction of bacterial lytic polysaccharide monooxygenases. Authors: Branch, J. / Rajagopal, B.S. / Paradisi, A. / Yates, N. / Lindley, P.J. / Smith, J. / Hollingsworth, K. / Turnbull, W.B. / Henrissat, B. / Parkin, A. / Berry, A. / Hemsworth, G.R. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7b21.cif.gz | 80.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7b21.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 7b21.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b2/7b21 ftp://data.pdbj.org/pub/pdb/validation_reports/b2/7b21 | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 10639.693 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Cellvibrio japonicus (strain Ueda107) (bacteria) Strain: Ueda107 / Gene: cbp2D, CJA_2616 / Production host: Escherichia coli (E. coli) / References: UniProt: B3PLJ6 | ||||
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#2: Chemical | ChemComp-HEC / | ||||
#3: Chemical | ChemComp-NA / | ||||
#4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.07 Å3/Da / Density % sol: 40.64 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.1 M HEPES pH 7.5, 20% w/v PEG 4000, 10% w/v propan-2-ol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: DIAMOND / Beamline: I03 / Wavelength: 0.976 Å | ||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 14, 2018 | ||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||
Radiation wavelength | Wavelength: 0.976 Å / Relative weight: 1 | ||||||||||||||||||
Reflection | Resolution: 1.2→55.85 Å / Num. obs: 28435 / % possible obs: 100 % / Redundancy: 6 % / CC1/2: 0.997 / Rmerge(I) obs: 0.05 / Rpim(I) all: 0.033 / Rrim(I) all: 0.06 / Net I/σ(I): 48.3 | ||||||||||||||||||
Reflection shell | CC1/2: 0.99 / Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.2→39.356 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.974 / WRfactor Rfree: 0.133 / WRfactor Rwork: 0.117 / SU B: 0.625 / SU ML: 0.013 / Average fsc free: 0.9838 / Average fsc work: 0.9872 / Cross valid method: THROUGHOUT / ESU R: 0.03 / ESU R Free: 0.029 Details: Hydrogens have been added in their riding positions
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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 BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 11.724 Å2
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Refinement step | Cycle: LAST / Resolution: 1.2→39.356 Å
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Refine LS restraints |
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LS refinement shell |
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