+Open data
-Basic information
Entry | Database: PDB / ID: 8prm | ||||||
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Title | The structure of nvBagel2 binding the P8W48O184 polyoxometalate | ||||||
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: 2.2 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 | 8prm.cif.gz | 83.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8prm.ent.gz | 62.9 KB | Display | PDB format |
PDBx/mmJSON format | 8prm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pr/8prm ftp://data.pdbj.org/pub/pdb/validation_reports/pr/8prm | HTTPS FTP |
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-Related structure data
Related structure data | 8pr9C 8prdC 8preC 8prfC 8prgC 8prhC 8priC 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.: 4 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 #2: Chemical | ChemComp-IR0 / | Mass: 12016.000 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: O184P8W48 / Feature type: SUBJECT OF INVESTIGATION #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.16 Å3/Da / Density % sol: 43.1 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion / pH: 8 Details: 0.1 M Tris pH 8.5, 5% (w/v) PEG 6000 (final pH 8.0) |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97242 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 28, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97242 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→46.11 Å / Num. obs: 30774 / % possible obs: 100 % / Redundancy: 12.2 % / CC1/2: 0.996 / Rmerge(I) obs: 0.156 / Rpim(I) all: 0.048 / Rrim(I) all: 0.164 / Χ2: 0.95 / Net I/σ(I): 11.4 |
Reflection shell | Resolution: 2.2→2.27 Å / % possible obs: 100 % / Redundancy: 13.6 % / Rmerge(I) obs: 0.837 / Num. measured all: 18768 / Num. unique obs: 1382 / CC1/2: 0.951 / Rpim(I) all: 0.236 / Rrim(I) all: 0.87 / Χ2: 0.76 / Net I/σ(I) obs: 3.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→39.91 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.98 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→39.91 Å
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Refine LS restraints |
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LS refinement shell |
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