+Open data
-Basic information
Entry | Database: PDB / ID: 8prg | ||||||
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Title | The structure of nvBagel6 | ||||||
Components | Cell surface protein | ||||||
Keywords | BIOSYNTHETIC PROTEIN / Protein design / symmetric / assembly / self-assembly / beta-propeller | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Dictyoglomus thermophilum (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å | ||||||
Authors | Vandebroek, L. / Voet, A.R.D. / Lee, X.Y. | ||||||
Funding support | Belgium, 1items
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Citation | Journal: To Be Published Title: The structure of v13Bagel2 Authors: Vandebroek, L. / Voet, A.R.D. / Lee, X.Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8prg.cif.gz | 29.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8prg.ent.gz | 17.3 KB | Display | PDB format |
PDBx/mmJSON format | 8prg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8prg_validation.pdf.gz | 415.6 KB | Display | wwPDB validaton report |
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Full document | 8prg_full_validation.pdf.gz | 415.5 KB | Display | |
Data in XML | 8prg_validation.xml.gz | 4.9 KB | Display | |
Data in CIF | 8prg_validation.cif.gz | 5.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pr/8prg ftp://data.pdbj.org/pub/pdb/validation_reports/pr/8prg | HTTPS FTP |
-Related structure data
Related structure data | 8pr9C 8prdC 8preC 8prfC 8prhC 8priC 8prmC 8proC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 9050.947 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Dictyoglomus thermophilum (bacteria) / Strain: ATCC 35947 / DSM 3960 / H-6-12 / Gene: DICTH_0179 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: B5YBJ6 |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.99 Å3/Da / Density % sol: 38.33 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion / pH: 4.6 Details: 0.17 M Ammonium sulfate, 0.085 M Sodium acetate pH 4.6, 25.5 %(w/v) PEG 2000 MME, 15 %(v/v) Glycerol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873128 Å |
Detector | Type: DECTRIS PILATUS3 X 2M / Detector: PIXEL / Date: Feb 14, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.873128 Å / Relative weight: 1 |
Reflection | Resolution: 2.35→38.52 Å / Num. obs: 3356 / % possible obs: 100 % / Redundancy: 14.6 % / CC1/2: 0.992 / Rmerge(I) obs: 0.292 / Rpim(I) all: 0.078 / Rrim(I) all: 0.303 / Χ2: 0.97 / Net I/σ(I): 12.6 |
Reflection shell | Resolution: 2.35→2.43 Å / % possible obs: 100 % / Redundancy: 15.6 % / Rmerge(I) obs: 1.069 / Num. measured all: 5094 / Num. unique obs: 326 / CC1/2: 0.864 / Rpim(I) all: 0.277 / Rrim(I) all: 1.106 / Χ2: 0.81 / Net I/σ(I) obs: 5.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.35→38.52 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.894 / SU B: 8.453 / SU ML: 0.198 / Cross valid method: THROUGHOUT / ESU R: 0.461 / ESU R Free: 0.266 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.88 Å2
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Refinement step | Cycle: 1 / Resolution: 2.35→38.52 Å
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Refine LS restraints |
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