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Yorodumi- PDB-1yjf: Cyclized post-translational product for S65A Y66S (GFPhal) green ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1yjf | |||||||||
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Title | Cyclized post-translational product for S65A Y66S (GFPhal) green fluorescent protein variant | |||||||||
Components | Green Fluorescent Protein | |||||||||
Keywords | LUMINESCENT PROTEIN / MIO / chromophore / electrophile / histidine ammonia lyase / HAL / biosynthesis / design | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | Aequorea victoria (jellyfish) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å | |||||||||
Authors | Barondeau, D.P. / Kassmann, C.J. / Tainer, J.A. / Getzoff, E.D. | |||||||||
Citation | Journal: Biochemistry / Year: 2005 Title: Understanding GFP Chromophore Biosynthesis: Controlling Backbone Cyclization and Modifying Post-translational Chemistry. Authors: Barondeau, D.P. / Kassmann, C.J. / Tainer, J.A. / Getzoff, E.D. #1: 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 | 1yjf.cif.gz | 70.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1yjf.ent.gz | 49.4 KB | Display | PDB format |
PDBx/mmJSON format | 1yjf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yj/1yjf ftp://data.pdbj.org/pub/pdb/validation_reports/yj/1yjf | HTTPS FTP |
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-Related 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: 26747.031 Da / Num. of mol.: 1 / Mutation: S65A, Y66S, F99S, M153T, V163A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aequorea victoria (jellyfish) / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)RIL / References: GenBank: 155661, UniProt: P42212*PLUS | ||
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#2: Chemical | #3: 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: 42 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8 Details: PEG4000, 50 mM MgCl2, 50 mM Hepes, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 11, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97 Å / Relative weight: 1 |
Reflection | Resolution: 1.35→50 Å / Num. obs: 49525 / % possible obs: 97.1 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Rsym value: 0.047 / Net I/σ(I): 21 |
Reflection shell | Resolution: 1.35→1.4 Å / Mean I/σ(I) obs: 2.7 / Rsym value: 0.338 / % possible all: 96 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.35→20 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 1.35→20 Å
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Refine LS restraints |
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