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Yorodumi- PDB-1z1p: Y66L variant of Enhanced Green Fluorescent Protein with 412-nm Ab... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1z1p | ||||||
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Title | Y66L variant of Enhanced Green Fluorescent Protein with 412-nm Absorbing Chromophore | ||||||
Components | green fluorescent protein | ||||||
Keywords | LUMINESCENT PROTEIN / GFP / Beta Barrel / UV/Vis absorbing yellow chromophore | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Aequorea victoria (jellyfish) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Rosenow, M.A. / Patel, H.N. / Wachter, R.M. | ||||||
Citation | Journal: Biochemistry / Year: 2005 Title: Oxidative Chemistry in the GFP Active Site Leads to Covalent Cross-Linking of a Modified Leucine Side Chain with a Histidine Imidazole: Implications for the Mechanism of Chromophore Formation. Authors: Rosenow, M.A. / Patel, H.N. / Wachter, R.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1z1p.cif.gz | 62.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1z1p.ent.gz | 44.7 KB | Display | PDB format |
PDBx/mmJSON format | 1z1p.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z1/1z1p ftp://data.pdbj.org/pub/pdb/validation_reports/z1/1z1p | HTTPS FTP |
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-Related structure data
Related structure data | 1z1qC 1s6zS 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: 26863.367 Da / Num. of mol.: 1 / Mutation: F64L, S65T, Y66L Source method: isolated from a genetically manipulated source Details: F64L, S65T, Y66L / Source: (gene. exp.) Aequorea victoria (jellyfish) / Plasmid: pRSETB / Production host: Escherichia coli (E. coli) / Strain (production host): JM109-DE3 / References: GenBank: 7428731, UniProt: P42212*PLUS |
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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: 2.17 Å3/Da / Density % sol: 42.86 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8 Details: PEG 8000, calcium acetate, sodium chloride, HEPES, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Mar 24, 2004 / Details: Osmic Confocal Mirrors |
Radiation | Monochromator: Ni Filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2→30 Å / Num. all: 14938 / Num. obs: 14782 / % possible obs: 95.3 % / Observed criterion σ(F): 4 / Observed criterion σ(I): 4 / Redundancy: 4.4 % / Biso Wilson estimate: 10.7 Å2 / Rmerge(I) obs: 0.103 / Net I/σ(I): 7.1 |
Reflection shell | Resolution: 2→2.13 Å / Rmerge(I) obs: 0.393 / Mean I/σ(I) obs: 2 / % possible all: 92.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB Entry 1S6Z Resolution: 2→28.74 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 1385116.61 / 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: 51.7359 Å2 / ksol: 0.427473 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2→28.74 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.13 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
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Xplor file |
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