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Yorodumi- PDB-8pxc: Structure of Fap1, a domain of the accessory Sec-dependent serine... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8pxc | ||||||
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Title | Structure of Fap1, a domain of the accessory Sec-dependent serine-rich glycoprotein adhesin from Streptococcus oralis, solved at wavelength 3.06 A | ||||||
Components | Fap1 | ||||||
Keywords | CELL ADHESION / Sec-dependent serine-rich glycoprotein adhesin | ||||||
Biological species | Streptococcus oralis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.973 Å | ||||||
Authors | El Omari, K. / Duman, R. / Mykhaylyk, V. / Orr, C. / Owen, C.D. / Walsh, M.A. / Wagner, A. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: Commun Chem / Year: 2023 Title: Experimental phasing opportunities for macromolecular crystallography at very long wavelengths. Authors: El Omari, K. / Duman, R. / Mykhaylyk, V. / Orr, C.M. / Latimer-Smith, M. / Winter, G. / Grama, V. / Qu, F. / Bountra, K. / Kwong, H.S. / Romano, M. / Reis, R.I. / Vogeley, L. / Vecchia, L. / ...Authors: El Omari, K. / Duman, R. / Mykhaylyk, V. / Orr, C.M. / Latimer-Smith, M. / Winter, G. / Grama, V. / Qu, F. / Bountra, K. / Kwong, H.S. / Romano, M. / Reis, R.I. / Vogeley, L. / Vecchia, L. / Owen, C.D. / Wittmann, S. / Renner, M. / Senda, M. / Matsugaki, N. / Kawano, Y. / Bowden, T.A. / Moraes, I. / Grimes, J.M. / Mancini, E.J. / Walsh, M.A. / Guzzo, C.R. / Owens, R.J. / Jones, E.Y. / Brown, D.G. / Stuart, D.I. / Beis, K. / Wagner, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8pxc.cif.gz | 120 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8pxc.ent.gz | 88.3 KB | Display | PDB format |
PDBx/mmJSON format | 8pxc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8pxc_validation.pdf.gz | 429.9 KB | Display | wwPDB validaton report |
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Full document | 8pxc_full_validation.pdf.gz | 430 KB | Display | |
Data in XML | 8pxc_validation.xml.gz | 13.7 KB | Display | |
Data in CIF | 8pxc_validation.cif.gz | 20.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/px/8pxc ftp://data.pdbj.org/pub/pdb/validation_reports/px/8pxc | HTTPS FTP |
-Related structure data
Related structure data | 8pwnC 8px0C 8px1C 8px4C 8px5C 8px7C 8px9C 8pxgC 8pxhC 8pxjC 8pxkC 8pxlC 8pyvC 8pyzC 8pz4C 8pz5C C: citing same article (ref.) |
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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: 48444.344 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus oralis (bacteria) / Production host: Escherichia coli (E. coli) | ||||||
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#2: Chemical | #3: Chemical | ChemComp-EDO / #4: 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: 1.51 Å3/Da / Density % sol: 54 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1 M BIS-Tris 5.5 25 % w/v PEG 3350 |
-Data collection
Diffraction | Mean temperature: 80 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I23 / Wavelength: 3.066 Å |
Detector | Type: DECTRIS PILATUS 12M / Detector: PIXEL / Date: May 25, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 3.066 Å / Relative weight: 1 |
Reflection | Resolution: 1.973→65.53 Å / Num. obs: 17626 / % possible obs: 84.33 % / Redundancy: 12.6 % / CC1/2: 0.99 / Rmerge(I) obs: 0.1122 / Rpim(I) all: 0.03096 / Rrim(I) all: 0.1169 / Net I/σ(I): 20.29 |
Reflection shell | Resolution: 1.973→2.043 Å / Mean I/σ(I) obs: 8.67 / Num. unique obs: 1321 / CC1/2: 0.962 |
-Processing
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Refinement | Method to determine structure: SAD / Resolution: 1.973→65.53 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.917 / SU B: 6.059 / SU ML: 0.094 / Cross valid method: THROUGHOUT / ESU R: 0.204 / ESU R Free: 0.17 / 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: 14.941 Å2
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Refinement step | Cycle: 1 / Resolution: 1.973→65.53 Å
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