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- PDB-4i38: Structures of IT intermediates from time-resolved laue crystallog... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4i38 | ||||||
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Title | Structures of IT intermediates from time-resolved laue crystallography collected at 14ID-B, APS | ||||||
![]() | Photoactive yellow protein![]() | ||||||
![]() | ![]() ![]() ![]() ![]() ![]() ![]() | ||||||
Function / homology | ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Jung, Y.O. / Lee, J.H. / Kim, J. / Schmidt, M. / Vukica, S. / Moffat, K. / Ihee, H. | ||||||
![]() | ![]() Title: Volume-conserving trans-cis isomerization pathways in photoactive yellow protein visualized by picosecond X-ray crystallography Authors: Jung, Y.O. / Lee, J.H. / Kim, J. / Schmidt, M. / Moffat, K. / Srajer, V. / Ihee, H. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 37.7 KB | Display | ![]() |
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PDB format | ![]() | 24.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3ve3C ![]() 3ve4C ![]() 4hy8C ![]() 4i39C ![]() 4i3aC ![]() 4i3iC ![]() 4i3jC ![]() 2phyS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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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.) ![]() ![]() ![]() ![]() ![]() |
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#2: Chemical | ChemComp-HC4 / ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.9 Å3/Da / Density % sol: 35.29 % |
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Crystal grow![]() | Temperature: 298 K / Method: hanging drop / pH: 7 Details: 2.6M AMMONIUM SULFATE, 50MM SODIUM PHOSPHATE, pH 7.0, hanging drop, temperature 298K |
-Data collection
Diffraction | Mean temperature: 288 K | |||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Nov 17, 2008 | |||||||||
Radiation | Protocol: LAUE / Monochromatic (M) / Laue (L): L / Scattering type: x-ray | |||||||||
Radiation wavelength |
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Reflection | Resolution: 1.6→28.9 Å / Num. obs: 14623 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: PDB ENTRY 2PHY Resolution: 1.6→10 Å / Num. parameters: 3952 / Num. restraintsaints: 4028 / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: FREE R / σ(F): 2 / Stereochemistry target values: ENGH AND HUBER Details: THE STRUCTURE FACTOR FILE REGARDING TO PDB FILE WAS BACK FOURIER-TRANSFORMED AND WAS EXTRAPOLATED FROM THE TIME-INDEPENDENT DIFFERENCE ELECTRON DENSITY MAP. THIS MAP WAS GENERATED USING ...Details: THE STRUCTURE FACTOR FILE REGARDING TO PDB FILE WAS BACK FOURIER-TRANSFORMED AND WAS EXTRAPOLATED FROM THE TIME-INDEPENDENT DIFFERENCE ELECTRON DENSITY MAP. THIS MAP WAS GENERATED USING KINETIC ANALYSIS BASED ON SEVERAL EXPERIMENTAL TIME-DEPENDENT DIFFERENCE ELECTRON DENSITY MAPS.
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Solvent computation | Solvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-228 | |||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 131.06 Å2 / Biso mean: 18.2623 Å2 / Biso min: 2.04 Å2 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.6→10 Å
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Refine LS restraints |
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