+Open data
-Basic information
Entry | Database: PDB / ID: 6p4i | ||||||
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Title | Photoactive Yellow Protein PYP 10ps | ||||||
Components | Photoactive yellow protein | ||||||
Keywords | SIGNALING PROTEIN / PYP / 10ps | ||||||
Function / homology | Function and homology information photoreceptor activity / phototransduction / regulation of DNA-templated transcription / identical protein binding Similarity search - Function | ||||||
Biological species | Halorhodospira halophila (bacteria) | ||||||
Method | X-RAY DIFFRACTION / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||
Authors | Pandey, S. / Schmidt, M. | ||||||
Funding support | United States, 1items
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Citation | Journal: Nat.Methods / Year: 2020 Title: Time-resolved serial femtosecond crystallography at the European XFEL. Authors: Pandey, S. / Bean, R. / Sato, T. / Poudyal, I. / Bielecki, J. / Cruz Villarreal, J. / Yefanov, O. / Mariani, V. / White, T.A. / Kupitz, C. / Hunter, M. / Abdellatif, M.H. / Bajt, S. / ...Authors: Pandey, S. / Bean, R. / Sato, T. / Poudyal, I. / Bielecki, J. / Cruz Villarreal, J. / Yefanov, O. / Mariani, V. / White, T.A. / Kupitz, C. / Hunter, M. / Abdellatif, M.H. / Bajt, S. / Bondar, V. / Echelmeier, A. / Doppler, D. / Emons, M. / Frank, M. / Fromme, R. / Gevorkov, Y. / Giovanetti, G. / Jiang, M. / Kim, D. / Kim, Y. / Kirkwood, H. / Klimovskaia, A. / Knoska, J. / Koua, F.H.M. / Letrun, R. / Lisova, S. / Maia, L. / Mazalova, V. / Meza, D. / Michelat, T. / Ourmazd, A. / Palmer, G. / Ramilli, M. / Schubert, R. / Schwander, P. / Silenzi, A. / Sztuk-Dambietz, J. / Tolstikova, A. / Chapman, H.N. / Ros, A. / Barty, A. / Fromme, P. / Mancuso, A.P. / Schmidt, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6p4i.cif.gz | 42.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6p4i.ent.gz | 26.7 KB | Display | PDB format |
PDBx/mmJSON format | 6p4i.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6p4i_validation.pdf.gz | 423.4 KB | Display | wwPDB validaton report |
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Full document | 6p4i_full_validation.pdf.gz | 426.4 KB | Display | |
Data in XML | 6p4i_validation.xml.gz | 8.7 KB | Display | |
Data in CIF | 6p4i_validation.cif.gz | 11.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p4/6p4i ftp://data.pdbj.org/pub/pdb/validation_reports/p4/6p4i | HTTPS FTP |
-Related structure data
Related structure data | 6p5dC 6p5eC 6p5fC 6p5gC 4wl9S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | |
Experimental dataset #1 | Data reference: 10.11577/1577287 / Data set type: diffraction image data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 14034.718 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Halorhodospira halophila (bacteria) / Gene: pyp / Production host: Escherichia coli (E. coli) / References: UniProt: P16113 |
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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: 1.88 Å3/Da / Density % sol: 34.5 % |
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Crystal grow | Temperature: 293 K / Method: small tubes / pH: 7 / Details: Sodium Malonate |
-Data collection
Diffraction | Mean temperature: 273 K / Serial crystal experiment: N |
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Diffraction source | Source: FREE ELECTRON LASER / Site: European XFEL / Beamline: SPB/SFX / Wavelength: 1.3 Å |
Detector | Type: AGIPD / Detector: PIXEL / Date: Mar 7, 2019 |
Radiation | Monochromator: European XFEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.3 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→11.15 Å / Num. obs: 12253 / % possible obs: 92.76 % / Redundancy: 284.4 % / Net I/σ(I): 11.77 |
Reflection shell | Resolution: 1.6→1.64 Å / Num. unique obs: 685 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4WL9 Resolution: 1.6→11.15 Å / Cor.coef. Fo:Fc: 0.844 / Cor.coef. Fo:Fc free: 0.776 / SU B: 4.924 / SU ML: 0.161 / Cross valid method: THROUGHOUT / ESU R: 0.179 / ESU R Free: 0.172 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 3.357 Å2
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Refinement step | Cycle: 1 / Resolution: 1.6→11.15 Å
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Refine LS restraints |
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