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Yorodumi- PDB-4wl9: Time Resolved Serial Femtosecond Crystallography Captures High Re... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4wl9 | ||||||
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Title | Time Resolved Serial Femtosecond Crystallography Captures High Resolution Intermediates of PYP | ||||||
Components | Photoactive yellow protein | ||||||
Keywords | SIGNALING PROTEIN / Dark structure / time-resolved serial femtosecond crystallography / Blue-light photoreceptor / nanocrystals / microcrystals | ||||||
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 | Tenboer, J. / Schmidt, M. | ||||||
Citation | Journal: Science / Year: 2014 Title: Time-resolved serial crystallography captures high-resolution intermediates of photoactive yellow protein. Authors: Tenboer, J. / Basu, S. / Zatsepin, N. / Pande, K. / Milathianaki, D. / Frank, M. / Hunter, M. / Boutet, S. / Williams, G.J. / Koglin, J.E. / Oberthuer, D. / Heymann, M. / Kupitz, C. / ...Authors: Tenboer, J. / Basu, S. / Zatsepin, N. / Pande, K. / Milathianaki, D. / Frank, M. / Hunter, M. / Boutet, S. / Williams, G.J. / Koglin, J.E. / Oberthuer, D. / Heymann, M. / Kupitz, C. / Conrad, C. / Coe, J. / Roy-Chowdhury, S. / Weierstall, U. / James, D. / Wang, D. / Grant, T. / Barty, A. / Yefanov, O. / Scales, J. / Gati, C. / Seuring, C. / Srajer, V. / Henning, R. / Schwander, P. / Fromme, R. / Ourmazd, A. / Moffat, K. / Van Thor, J.J. / Spence, J.C. / Fromme, P. / Chapman, H.N. / Schmidt, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4wl9.cif.gz | 42.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4wl9.ent.gz | 27.5 KB | Display | PDB format |
PDBx/mmJSON format | 4wl9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wl/4wl9 ftp://data.pdbj.org/pub/pdb/validation_reports/wl/4wl9 | HTTPS FTP |
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-Related structure data
Related structure data | 4wlaC 2phyS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 13888.575 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: Chemical | ChemComp-HC4 / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 110956 |
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-Sample preparation
Crystal | Density Matthews: 1.9 Å3/Da / Density % sol: 35.19 % / Description: Rsplit=0.065 |
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Crystal grow | Temperature: 296 K / Method: batch mode / pH: 7 Details: Microcrystals (~ 2 x 2 x 5 um^3) were formed by centrifugation in a spin filter. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: FREE ELECTRON LASER / Site: SLAC LCLS / Beamline: CXI / Wavelength: 1.3784 Å |
Detector | Type: CS-PAD detector / Detector: PIXEL / Date: Jun 6, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.3784 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→16.73 Å / Num. obs: 13500 / % possible obs: 100 % / Redundancy: 1500 % / R split: 0.065 / Net I/σ(I): 12.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2PHY Resolution: 1.6→16.73 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.916 / SU B: 1.548 / SU ML: 0.058 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.118 / ESU R Free: 0.111 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : REFINED INDIVIDUALLY
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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 max: 76.1 Å2 / Biso mean: 18.943 Å2 / Biso min: 8.15 Å2
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Refinement step | Cycle: final / Resolution: 1.6→16.73 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.6→1.641 Å / Total num. of bins used: 20
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