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Yorodumi- PDB-5hdc: Femtosecond Structural Dynamics Drives the Trans/Cis Isomerizatio... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5hdc | |||||||||
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Title | Femtosecond Structural Dynamics Drives the Trans/Cis Isomerization in Photoactive Yellow Protein: 100 fs to 400 fs Structure | |||||||||
Components | Photoactive yellow protein | |||||||||
Keywords | SIGNALING PROTEIN / PHOTORECEPTOR CIS TRANS ISOMERIZATION / TRANS CIS ISOMERIZATION / FREE ELECTRON LASER | |||||||||
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 / Resolution: 1.6 Å | |||||||||
Authors | Pande, K. / Tenboer, J. / Schmidt, M. | |||||||||
Funding support | United States, 2items
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Citation | Journal: Science / Year: 2016 Title: Femtosecond structural dynamics drives the trans/cis isomerization in photoactive yellow protein. Authors: Pande, K. / Hutchison, C.D. / Groenhof, G. / Aquila, A. / Robinson, J.S. / Tenboer, J. / Basu, S. / Boutet, S. / DePonte, D.P. / Liang, M. / White, T.A. / Zatsepin, N.A. / Yefanov, O. / ...Authors: Pande, K. / Hutchison, C.D. / Groenhof, G. / Aquila, A. / Robinson, J.S. / Tenboer, J. / Basu, S. / Boutet, S. / DePonte, D.P. / Liang, M. / White, T.A. / Zatsepin, N.A. / Yefanov, O. / Morozov, D. / Oberthuer, D. / Gati, C. / Subramanian, G. / James, D. / Zhao, Y. / Koralek, J. / Brayshaw, J. / Kupitz, C. / Conrad, C. / Roy-Chowdhury, S. / Coe, J.D. / Metz, M. / Xavier, P.L. / Grant, T.D. / Koglin, J.E. / Ketawala, G. / Fromme, R. / Srajer, V. / Henning, R. / Spence, J.C. / Ourmazd, A. / Schwander, P. / Weierstall, U. / Frank, M. / Fromme, P. / Barty, A. / Chapman, H.N. / Moffat, K. / van Thor, J.J. / Schmidt, M. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5hdc.cif.gz | 41.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5hdc.ent.gz | 27.7 KB | Display | PDB format |
PDBx/mmJSON format | 5hdc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5hdc_validation.pdf.gz | 425.9 KB | Display | wwPDB validaton report |
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Full document | 5hdc_full_validation.pdf.gz | 428 KB | Display | |
Data in XML | 5hdc_validation.xml.gz | 8.5 KB | Display | |
Data in CIF | 5hdc_validation.cif.gz | 11.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hd/5hdc ftp://data.pdbj.org/pub/pdb/validation_reports/hd/5hdc | HTTPS FTP |
-Related structure data
Related structure data | 5hd3C 5hd5C 5hddC 5hdsC C: citing same article (ref.) |
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Similar structure data | |
Experimental dataset #1 | Data reference: 10.11577/1573793 / 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: 295 K / Method: liquid diffusion / pH: 7 Details: Combine and vortex 4.45M sodium malonate with 100 uL protein (135 mg/ml initial concentration) for a final sodium malonate concentration of 3.2M. Let stand at room temperature for 1 hour. ...Details: Combine and vortex 4.45M sodium malonate with 100 uL protein (135 mg/ml initial concentration) for a final sodium malonate concentration of 3.2M. Let stand at room temperature for 1 hour. Spin at 10,000g for 2 hours in small spin concentrators. Vortex and let stand at room temperature for 4 hours. Harvest crystals and rebuffer with 3.0M sodium malonate. PH range: 6.95-7.05 / Temp details: Ambient Room Temperature |
-Data collection
Diffraction | Mean temperature: 295 K Ambient temp details: Injection of crystals into vacuum. No temperature control. |
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Diffraction source | Source: FREE ELECTRON LASER / Site: SLAC LCLS / Beamline: CXI / Wavelength: 1.31 Å |
Detector | Type: CS-PAD CXI-1 / Detector: PIXEL / Date: Mar 18, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.31 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→19.31 Å / Num. all: 13039 / Num. obs: 13039 / % possible obs: 98.72 % / Redundancy: 300 % / Net I/σ(I): 10 |
-Processing
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Refinement | Resolution: 1.6→19.31 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.887 / SU B: 3.719 / SU ML: 0.119 / Cross valid method: THROUGHOUT / ESU R: 0.123 / ESU R Free: 0.123 / 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: 5.462 Å2
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Refinement step | Cycle: LAST / Resolution: 1.6→19.31 Å
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Refine LS restraints |
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