+Open data
-Basic information
Entry | Database: PDB / ID: 8prp | ||||||
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Title | The structure of nvBagel2 in the presence of Cd(II) | ||||||
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: 2.82 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 nvBagel2 in the presence of Cd(II) 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 | 8prp.cif.gz | 29.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8prp.ent.gz | 17.1 KB | Display | PDB format |
PDBx/mmJSON format | 8prp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8prp_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 8prp_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 8prp_validation.xml.gz | 4.8 KB | Display | |
Data in CIF | 8prp_validation.cif.gz | 5.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pr/8prp ftp://data.pdbj.org/pub/pdb/validation_reports/pr/8prp | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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-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 (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: Chemical | #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.29 Å3/Da / Density % sol: 46.22 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion / pH: 7.5 Details: 0.0425 M Cadmium sulfate, 0.085 M HEPES pH 7.5, 0.85 M Sodium acetate, 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: I04 / Wavelength: 0.69 Å |
Detector | Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Dec 9, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.69 Å / Relative weight: 1 |
Reflection | Resolution: 2.82→31.7 Å / Num. obs: 2236 / % possible obs: 100 % / Redundancy: 24.2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.163 / Rpim(I) all: 0.034 / Rrim(I) all: 0.166 / Net I/σ(I): 18.3 / Num. measured all: 54030 |
Reflection shell | Resolution: 2.82→2.87 Å / % possible obs: 99.1 % / Redundancy: 14.2 % / Rmerge(I) obs: 1.138 / Num. measured all: 1596 / Num. unique obs: 112 / CC1/2: 0.873 / Rpim(I) all: 0.306 / Rrim(I) all: 1.18 / Net I/σ(I) obs: 2.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.82→31.7 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.94 / Phase error: 19.41 / Stereochemistry target values: MLHL
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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: 2.82→31.7 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.82→31.7 Å
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