+Open data
-Basic information
Entry | Database: PDB / ID: 1c4f | ||||||
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Title | GREEN FLUORESCENT PROTEIN S65T AT PH 4.6 | ||||||
Components | GREEN FLUORESCENT PROTEIN | ||||||
Keywords | SIGNALING PROTEIN / GREENFLUORESCENT PROTEIN / BIOLUMINESCENCE / PHOTOACTIVE PROTEIN / FLUORESCENT TAG / PH TITRATION | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Aequorea victoria (jellyfish) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å | ||||||
Authors | Elsliger, M.A. / Wachter, R.M. / Kallio, K. / Hanson, G.T. / Remington, S.J. | ||||||
Citation | Journal: Biochemistry / Year: 1999 Title: Structural and spectral response of green fluorescent protein variants to changes in pH. Authors: Elsliger, M.A. / Wachter, R.M. / Hanson, G.T. / Kallio, K. / Remington, S.J. #1: Journal: Structure / Year: 1998 Title: Structural Basis of Spectral Shifts in the Yellow-Emission Variants of Green Fluorescent Protein Authors: Wachter, R.M. / Elsliger, M.A. / Kallio, K. / Hanson, G.T. / Remington, S.J. #2: Journal: Biochemistry / Year: 1997 Title: Crystal Structure and Photodynamic Behavior of the Blue Emission Variant Y66H/ Y145F of Green Fluorescent Protein Authors: Wachter, R.M. / King, B.A. / Heim, R. / Kallio, K. / Tsien, R.Y. / Boxer, S.G. / Remington, S.J. #3: Journal: Science / Year: 1996 Title: Crystal Structure of the Aequorea Victoria Green Fluorescent Protein Authors: Ormo, M. / Cubitt, A.B. / Kallio, K. / Gross, L.A. / Tsien, R.Y. / Remington, S.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1c4f.cif.gz | 60.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1c4f.ent.gz | 42.1 KB | Display | PDB format |
PDBx/mmJSON format | 1c4f.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c4/1c4f ftp://data.pdbj.org/pub/pdb/validation_reports/c4/1c4f | HTTPS FTP |
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-Related structure data
Related structure data | 1emgC 1emaS S: Starting model for refinement 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: 26945.383 Da / Num. of mol.: 1 Mutation: 65 - 67 REPLACED BY CRO, S65T SUBSTITUTION, Q80R SUBSTITUTION Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aequorea victoria (jellyfish) / Tissue: CIRCUMORAL RING CANAL / Description: THE N-TERMINAL HIS-TAG HAS BEEN REMOVED / Organ: PHOTOGENIC ORGAN / Cellular location (production host): CYTOPLASM / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 (DE3) / References: UniProt: P42212 |
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#2: Water | ChemComp-HOH / |
Sequence details | RESIDUES 1-3 NOT SEEN IN DENSITY MAPS RESIDUES 230-238 NOT SEEN IN DENSITY MAPS THE FLUOROPHORE ...RESIDUES 1-3 NOT SEEN IN DENSITY MAPS RESIDUES 230-238 NOT SEEN IN DENSITY MAPS THE FLUOROPHOR |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.1 Å3/Da / Density % sol: 41.34 % | ||||||||||||||||||||||||||||||
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 4.6 Details: 10-13% PEG 3400, 100MM SODIUM ACETATE AND 100 MM AMMONIUM ACETATE, pH 4.6, VAPOR DIFFUSION, HANGING DROP | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 295 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X12B / Wavelength: 1.54 |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.25→24.3 Å / Num. obs: 14685 / % possible obs: 96 % / Observed criterion σ(I): 2 / Redundancy: 4 % / Biso Wilson estimate: 34 Å2 / Rmerge(I) obs: 0.058 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1EMA Resolution: 2.25→24 Å / Isotropic thermal model: TNT / σ(F): 0 / Stereochemistry target values: TNT
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Solvent computation | Solvent model: BABINET SCALING / Bsol: 140 Å2 / ksol: 0.822 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.25→24 Å
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Refine LS restraints |
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Software | *PLUS Name: TNT / Version: 5F / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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