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Yorodumi- PDB-3ve3: Structure of IT Intermediate from time-resolved laue crystallography -
+Open data
-Basic information
Entry | Database: PDB / ID: 3ve3 | ||||||
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Title | Structure of IT Intermediate from time-resolved laue crystallography | ||||||
Components | Photoactive yellow protein | ||||||
Keywords | LUMINESCENT PROTEIN / PHOTORECEPTOR / CHROMOPHORE / SENSORY TRANSDUCTION | ||||||
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 / SYNCHROTRON / AB INITIO PHASING / Resolution: 1.6 Å | ||||||
Authors | Ihee, H. / Jung, Y.O. | ||||||
Citation | Journal: NAT.CHEM. / Year: 2013 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3ve3.cif.gz | 32.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ve3.ent.gz | 24.3 KB | Display | PDB format |
PDBx/mmJSON format | 3ve3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ve/3ve3 ftp://data.pdbj.org/pub/pdb/validation_reports/ve/3ve3 | HTTPS FTP |
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-Related structure data
Related structure data | 3ve4C 4hy8C 4i38C 4i39C 4i3aC 4i3iC 4i3jC C: citing same article (ref.) |
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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 / Plasmid: PQE80 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): M15 / References: UniProt: P16113 |
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#2: Chemical | ChemComp-HC4 / |
Nonpolymer details | HC4 IS A CHROMOPHOR |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: vapor diffusion, hanging drop / pH: 7 Details: 2.6M AMMONIUM SULFATE, 50MM SODIUM PHOSPHATE, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 288 K | |||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID09 / Wavelength: 0.77-1.24 | |||||||||
Detector | Type: MAR CCD 130 mm / Detector: CCD / Date: Oct 15, 2005 | |||||||||
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: 13891 |
-Processing
Software |
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Refinement | Method to determine structure: AB INITIO PHASING / Resolution: 1.6→10 Å / Num. parameters: 3952 / Num. restraintsaints: 4021 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: Engh & 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 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.6→10 Å
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Refine LS restraints |
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