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Yorodumi- PDB-1huy: CRYSTAL STRUCTURE OF CITRINE, AN IMPROVED YELLOW VARIANT OF GREEN... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1huy | ||||||
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Title | CRYSTAL STRUCTURE OF CITRINE, AN IMPROVED YELLOW VARIANT OF GREEN FLUORESCENT PROTEIN | ||||||
Components | GREEN FLUORESCENT PROTEIN | ||||||
Keywords | LUMINESCENT PROTEIN / beta barrel / chromophore | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Aequorea victoria (jellyfish) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Griesbeck, O. / Baird, G.S. / Campbell, R.E. / Zacharias, D.A. / Tsien, R.Y. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2001 Title: Reducing the environmental sensitivity of yellow fluorescent protein. Mechanism and applications Authors: Griesbeck, O. / Baird, G.S. / Campbell, R.E. / Zacharias, D.A. / Tsien, R.Y. | ||||||
History |
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Remark 600 | HETEROGEN THE HET RESIDUE CRO IS FORMED FROM AN AUTOCATALYTIC POST-TRANSLATIONAL CYCLIZATION, ...HETEROGEN THE HET RESIDUE CRO IS FORMED FROM AN AUTOCATALYTIC POST-TRANSLATIONAL CYCLIZATION, DEHYDRATION, AND OXIDATION OF RESIDUES GLY 65, TYR 66, AND GLY 67, RESULTING IN A COVALENTLY LINKED GREEN CHROMOPHORE. | ||||||
Remark 999 | SEQUENCE RESIDUES GLY65, TYR66, AND GLY67 ARE NOT PRESENT IN THE ENTRY. INSTEAD THEY ARE REPLACED ...SEQUENCE RESIDUES GLY65, TYR66, AND GLY67 ARE NOT PRESENT IN THE ENTRY. INSTEAD THEY ARE REPLACED WITH CRO66. The GFP chromophore (CRO) is formed from cyclization of the main chain of residues Gly65, Tyr66, and Gly67. A subsequent oxidation of the Tyr66 side chain yields the mature chromophore. The N-terminal addition of an Asp and a Pro residue results from Enterokinase catalyzed cleavage of a His tag that facilitated purification. Val 1A is inserted to improve expression in mammalian systems. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1huy.cif.gz | 61.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1huy.ent.gz | 44.1 KB | Display | PDB format |
PDBx/mmJSON format | 1huy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1huy_validation.pdf.gz | 431.5 KB | Display | wwPDB validaton report |
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Full document | 1huy_full_validation.pdf.gz | 433.1 KB | Display | |
Data in XML | 1huy_validation.xml.gz | 11.7 KB | Display | |
Data in CIF | 1huy_validation.cif.gz | 15.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hu/1huy ftp://data.pdbj.org/pub/pdb/validation_reports/hu/1huy | HTTPS FTP |
-Related structure data
Related structure data | 2yfpS S: Starting model for refinement |
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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: 27319.883 Da / Num. of mol.: 1 / Mutation: S65G, V68L, Q69M, S72A, T203Y Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aequorea victoria (jellyfish) / Gene: GFP / Plasmid: PRSETB / Production host: Escherichia coli (E. coli) / Strain (production host): JM109(DE3) / 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: 2.1 Å3/Da / Density % sol: 41.36 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5 Details: 50 mM NH4OAc, 50 mM NaOAc, 8% PEG 3400, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 17, 2000 / Details: mirrors |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→50 Å / Num. all: 12193 / Num. obs: 12106 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.8 % / Biso Wilson estimate: 14.4 Å2 / Rmerge(I) obs: 0.055 / Net I/σ(I): 32.6 |
Reflection shell | Resolution: 2.2→2.28 Å / Redundancy: 4 % / Rmerge(I) obs: 0.144 / Mean I/σ(I) obs: 10.3 / Num. unique all: 1181 / % possible all: 99.7 |
Reflection | *PLUS Lowest resolution: 28.3 Å |
Reflection shell | *PLUS % possible obs: 99.7 % / Num. unique obs: 1181 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2YFP Resolution: 2.2→28.3 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 1263802.3 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 32.57 Å2 / ksol: 0.3133 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.2→28.3 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.28 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 10
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Xplor file |
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Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS σ(F): 0 / % reflection Rfree: 10.4 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 28.2 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.26 / % reflection Rfree: 11.9 % / Rfactor Rwork: 0.195 |