+Open data
-Basic information
Entry | Database: PDB / ID: 1yhi | ||||||
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Title | Uncyclized precursor structure of S65A Y66S R96A GFP variant | ||||||
Components | Green Fluorescent Protein | ||||||
Keywords | LUMINESCENT PROTEIN / Chromophore / uncyclized | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Aequorea victoria (jellyfish) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Barondeau, D.P. / Kassmann, C.J. / Tainer, J.A. / Getzoff, E.D. | ||||||
Citation | Journal: Biochemistry / Year: 2005 Title: Understanding GFP Chromophore Biosynthesis: Controlling Backbone Cyclization and Modifying Post-translational Chemistry(,). Authors: Barondeau, D.P. / Kassmann, C.J. / Tainer, J.A. / Getzoff, E.D. #1: Journal: Proc.Natl.Acad.Sci.USA / Year: 2003 Title: Mechanism and Energetics of Green Fluorescent Protein Chromophore Synthesis Revealed by Trapped Intermediate Structures Authors: Barondeau, D.P. / Putnam, C.D. / Kassmann, C.J. / Tainer, J.A. / Getzoff, E.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1yhi.cif.gz | 59.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1yhi.ent.gz | 42 KB | Display | PDB format |
PDBx/mmJSON format | 1yhi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1yhi_validation.pdf.gz | 419.7 KB | Display | wwPDB validaton report |
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Full document | 1yhi_full_validation.pdf.gz | 419.7 KB | Display | |
Data in XML | 1yhi_validation.xml.gz | 11.1 KB | Display | |
Data in CIF | 1yhi_validation.cif.gz | 15.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yh/1yhi ftp://data.pdbj.org/pub/pdb/validation_reports/yh/1yhi | HTTPS FTP |
-Related 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: 26696.949 Da / Num. of mol.: 1 / Mutation: S65A, Y66S, R96A, F99S, M153T, V163A Source method: isolated from a genetically manipulated source Details: S65A, Y66S, R96A, F99S, M153T, V163A / Source: (gene. exp.) Aequorea victoria (jellyfish) / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)RIL / References: UniProt: P42212 |
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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: 2.3 Å3/Da / Density % sol: 46.6 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8 Details: PEG4000, 50 mM MgCl2, 50 mM Hepes, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.984 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 2, 2003 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.984 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.9→50 Å / Num. obs: 19956 / % possible obs: 98.6 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Rmerge(I) obs: 0.059 / Χ2: 1.097 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→50 Å / Data cutoff high absF: 10000 / Data cutoff low absF: 0 / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 48.259 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→50 Å
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Refine LS restraints |
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