+Open data
-Basic information
Entry | Database: PDB / ID: 8prh | ||||||
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Title | The structure of nvBagel7 | ||||||
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: 1.6 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 | 8prh.cif.gz | 30.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8prh.ent.gz | 18.4 KB | Display | PDB format |
PDBx/mmJSON format | 8prh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8prh_validation.pdf.gz | 422.2 KB | Display | wwPDB validaton report |
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Full document | 8prh_full_validation.pdf.gz | 422.8 KB | Display | |
Data in XML | 8prh_validation.xml.gz | 5.9 KB | Display | |
Data in CIF | 8prh_validation.cif.gz | 7.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pr/8prh ftp://data.pdbj.org/pub/pdb/validation_reports/pr/8prh | HTTPS FTP |
-Related structure data
Related structure data | 8pr9C 8prdC 8preC 8prfC 8prgC 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 on special symmetry positions |
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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 (strain ATCC 35947 / DSM 3960 / H-6-12) (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: 2 Å3/Da / Density % sol: 38.35 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion / pH: 5.6 Details: 0.17 M Ammonium acetate, 0.085 M tri-Sodium citrate pH 5.6, 25.5 %(w/v) PEG 4000, 15 %(v/v) Glycerol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å |
Detector | Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Jul 30, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→54.13 Å / Num. obs: 10181 / % possible obs: 100 % / Redundancy: 24 % / CC1/2: 1 / Rmerge(I) obs: 0.056 / Rpim(I) all: 0.011 / Rrim(I) all: 0.057 / Net I/σ(I): 38.3 / Num. measured all: 244109 |
Reflection shell | Resolution: 1.6→1.63 Å / % possible obs: 100 % / Redundancy: 18.6 % / Rmerge(I) obs: 0.243 / Num. measured all: 9268 / Num. unique obs: 499 / CC1/2: 0.988 / Rpim(I) all: 0.057 / Rrim(I) all: 0.25 / Net I/σ(I) obs: 6.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→38.28 Å / SU ML: 0.1 / Cross valid method: FREE R-VALUE / σ(F): 1.45 / Phase error: 18.87 / Stereochemistry target values: MLHL
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.6→38.28 Å
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Refine LS restraints |
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LS refinement shell |
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