+Open data
-Basic information
Entry | Database: PDB / ID: 1yfp | ||||||
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Title | STRUCTURE OF YELLOW-EMISSION VARIANT OF GFP | ||||||
Components | YELLOW FLUORESCENT PROTEIN | ||||||
Keywords | LUMINESCENCE / GREEN FLUORESCENT PROTEIN / YELLOW-EMISSION VARIANT / BIOLUMINESCENCE / PHOTOACTIVE PROTEIN / FLUORESCENT TAG | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Aequorea victoria (jellyfish) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Wachter, R.M. / Elsliger, M.-A. / Kallio, K. / Hanson, G.T. / Remington, S.J. | ||||||
Citation | 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. | ||||||
History |
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Remark 999 | THE CHROMOPHORE CRO IS GENERATED BY AN AUTOCATALYTIC CYCLIZATION OF THE POLYPEPTIDE BACKBONE OF SER ...THE CHROMOPHORE CRO IS GENERATED BY AN AUTOCATALYTIC CYCLIZATION OF THE POLYPEPTIDE BACKBONE OF SER 65, TYR 66, GLY 67. RESIDUES SER65 under went mutation to GLY65 before cyclization. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1yfp.cif.gz | 94.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1yfp.ent.gz | 75.2 KB | Display | PDB format |
PDBx/mmJSON format | 1yfp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1yfp_validation.pdf.gz | 430.2 KB | Display | wwPDB validaton report |
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Full document | 1yfp_full_validation.pdf.gz | 440 KB | Display | |
Data in XML | 1yfp_validation.xml.gz | 19.9 KB | Display | |
Data in CIF | 1yfp_validation.cif.gz | 25.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yf/1yfp ftp://data.pdbj.org/pub/pdb/validation_reports/yf/1yfp | HTTPS FTP |
-Related structure data
Related structure data | 2yfpC 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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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.99998, -0.00309, -0.00619), Vector: |
-Components
#1: Protein | Mass: 25709.994 Da / Num. of mol.: 2 / Mutation: S65G, V68L, S72A, Q80R, H148G, T203Y Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aequorea victoria (jellyfish) / Tissue: CIRCUMORAL RING CANAL / Gene: GFP / Organ: PHOTOGENIC ORGAN / Plasmid: PRSETB (INVITROGEN) / Cellular location (production host): CYTOPLASM / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 (DE3) / References: UniProt: P42212 #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 2.66 Å3/Da / Density % sol: 53.4 % / Description: ISOMORPHOUS REPLACEMENT | ||||||||||||||||||||
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Crystal grow | Temperature: 288 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: YFP WAS CONCENTRATED TO 10 MG/ML IN 50 MM HEPES PH 7.5. ROD-SHAPED CRYSTALS WITH APPROXIMATE DIMENSIONS OF 0.8 X 0.12 X 0.03 MM WERE GROWN IN HANGING DROPS CONTAINING 5 MICROLITERS PROTEIN ...Details: YFP WAS CONCENTRATED TO 10 MG/ML IN 50 MM HEPES PH 7.5. ROD-SHAPED CRYSTALS WITH APPROXIMATE DIMENSIONS OF 0.8 X 0.12 X 0.03 MM WERE GROWN IN HANGING DROPS CONTAINING 5 MICROLITERS PROTEIN AND 5 MICROLITERS MOTHER LIQUOR AT 15 DEGREES C AFTER 2 WEEKS. THE MOTHER LIQUOR CONTAINED 2.2 M SODIUM/POTASSIUM PHOSPHATE PH 6.9., vapor diffusion - hanging drop, temperature 288K | ||||||||||||||||||||
Crystal | *PLUS | ||||||||||||||||||||
Crystal grow | *PLUS Temperature: 15 ℃ / Method: vapor diffusion, hanging drop | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 295 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 |
Detector | Type: RIGAKU / Detector: IMAGE PLATE / Date: Dec 5, 1997 / Details: MIRRORS |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→20 Å / Num. obs: 18916 / % possible obs: 92 % / Observed criterion σ(I): 1.9 / Redundancy: 4 % / Biso Wilson estimate: 28.2 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 10.8 |
Reflection shell | Resolution: 2.5→2.56 Å / Redundancy: 4 % / % possible all: 94 |
Reflection | *PLUS Num. measured all: 53039 / Rmerge(I) obs: 0.08 |
Reflection shell | *PLUS % possible obs: 94 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1EMA Resolution: 2.5→20 Å / Isotropic thermal model: TNT / Stereochemistry target values: TNT
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Solvent computation | Bsol: 150 Å2 / ksol: 0.82 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→20 Å
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Refine LS restraints |
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Software | *PLUS Name: TNT / Version: 5F / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.192 | ||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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