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Yorodumi- PDB-1qyo: Anaerobic precylization intermediate crystal structure for S65G Y... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1qyo | ||||||
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Title | Anaerobic precylization intermediate crystal structure for S65G Y66G GFP variant | ||||||
Components | green-fluorescent protein | ||||||
Keywords | LUMINESCENT PROTEIN / beta barrel / chromophore / trapped intermediate | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Aequorea victoria (jellyfish) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Barondeau, D.P. / Putnam, C.D. / Kassmann, C.J. / Tainer, J.A. / Getzoff, E.D. | ||||||
Citation | 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 | 1qyo.cif.gz | 65.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1qyo.ent.gz | 47.2 KB | Display | PDB format |
PDBx/mmJSON format | 1qyo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qy/1qyo ftp://data.pdbj.org/pub/pdb/validation_reports/qy/1qyo | HTTPS FTP |
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-Related structure data
Related structure data | 1qxtC 1qy3C 1qyfC 1qyqC 1emaS C: citing same article (ref.) 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: 26633.918 Da / Num. of mol.: 1 / Mutation: F99S, M153T, V163A, F64L, S65G, Y66G Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aequorea victoria (jellyfish) / Gene: GFP / Plasmid: pET11a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(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: 2.15 Å3/Da / Density % sol: 42.81 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8 Details: PEG 4000, Magnesium Chloride, Hepes, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: SIEMENS / Wavelength: 1.54179 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 2, 2002 |
Radiation | Monochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54179 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→20 Å / Num. all: 21947 / Num. obs: 21270 / % possible obs: 96.5 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Biso Wilson estimate: 13.2 Å2 / Rsym value: 0.072 / Net I/σ(I): 20.2 |
Reflection shell | Resolution: 1.8→1.86 Å / Mean I/σ(I) obs: 3.4 / Rsym value: 0.366 / % possible all: 85.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1ema Resolution: 1.8→17.44 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 493845.43 / Data cutoff high rms absF: 493845.43 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 20.5896 Å2 / ksol: 0.35782 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.8→17.44 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.91 Å / Rfactor Rfree error: 0.028 / Total num. of bins used: 6
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Xplor file |
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