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Yorodumi- PDB-1yj2: Cyclized, non-dehydrated post-translational product for S65A Y66S... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1yj2 | ||||||
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Title | Cyclized, non-dehydrated post-translational product for S65A Y66S H148G GFP variant | ||||||
Components | Green Fluorescent Protein | ||||||
Keywords | LUMINESCENT PROTEIN / MIO / chromophore / electrophile / histidine / ammonia / lyase / HAL / biosynthesis | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Aequorea victoria (jellyfish) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 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 | 1yj2.cif.gz | 64.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1yj2.ent.gz | 50.2 KB | Display | PDB format |
PDBx/mmJSON format | 1yj2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1yj2_validation.pdf.gz | 437.5 KB | Display | wwPDB validaton report |
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Full document | 1yj2_full_validation.pdf.gz | 439 KB | Display | |
Data in XML | 1yj2_validation.xml.gz | 15.5 KB | Display | |
Data in CIF | 1yj2_validation.cif.gz | 24.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yj/1yj2 ftp://data.pdbj.org/pub/pdb/validation_reports/yj/1yj2 | HTTPS FTP |
-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: 26683.951 Da / Num. of mol.: 1 / Mutation: S65A Y66S F99S H148G 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 | ChemComp-MG / |
#3: Chemical | ChemComp-EDO / |
#4: 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: 1 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 28, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→30 Å / Num. obs: 36704 / % possible obs: 98 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Rsym value: 0.061 / Net I/σ(I): 16 |
Reflection shell | Resolution: 1.5→1.55 Å / Mean I/σ(I) obs: 2.8 / Rsym value: 0.372 / % possible all: 91.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→20 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 1.5→20 Å
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Refine LS restraints |
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