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Yorodumi- PDB-1jc1: CRYSTAL STRUCTURE ANALYSIS OF A REDOX-SENSITIVE GREEN FLUORESCENT... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1jc1 | ||||||
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Title | CRYSTAL STRUCTURE ANALYSIS OF A REDOX-SENSITIVE GREEN FLUORESCENT PROTEIN VARIANT IN A OXIDIZED FORM | ||||||
Components | GREEN FLUORESCENT PROTEIN | ||||||
Keywords | LUMINESCENT PROTEIN / Beta Barrel / Chromophore / Disulfide Bond | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Aequorea victoria (jellyfish) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Hanson, G.T. / Aggeler, R. / Oglesbee, D. / Cannon, M. / Capaldi, R.A. / Tsien, R.Y. / Remington, S.J. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2004 Title: Investigating mitochondrial redox potential with redox-sensitive green fluorescent protein indicators. Authors: Hanson, G.T. / Aggeler, R. / Oglesbee, D. / Cannon, M. / Capaldi, R.A. / Tsien, R.Y. / Remington, S.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1jc1.cif.gz | 148.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1jc1.ent.gz | 115.2 KB | Display | PDB format |
PDBx/mmJSON format | 1jc1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jc/1jc1 ftp://data.pdbj.org/pub/pdb/validation_reports/jc/1jc1 | HTTPS FTP |
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-Related structure data
Related structure data | 1jc0C 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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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 26886.379 Da / Num. of mol.: 3 / Mutation: C48S,F64L,S65T,Q80R,S147C,Q204C Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aequorea victoria (jellyfish) / Plasmid: pRSETb / Production host: Escherichia coli (E. coli) / Strain (production host): JM109(DE3) / References: UniProt: P42212 #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 43.99 % | |||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: PEG 4000, Lithium Sulfate, Tris, Copper (II) Chloride, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K | |||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7.9 / Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Nov 25, 2000 Details: 58 cm long, Pt-coated fused silica, vertical focus mirror |
Radiation | Monochromator: Cylindrically bent triangular Si(111) asymmetric cut horizontal focus Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.08 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→29.7 Å / Num. all: 203865 / Num. obs: 56854 / % possible obs: 99.8 % / Redundancy: 3.6 % / Biso Wilson estimate: 27.7 Å2 / Rmerge(I) obs: 0.058 / Net I/σ(I): 7.2 |
Reflection shell | Resolution: 1.9→1.94 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.314 / Mean I/σ(I) obs: 2.3 / Num. unique all: 4181 / % possible all: 100 |
Reflection | *PLUS Num. measured all: 203865 |
Reflection shell | *PLUS Lowest resolution: 1.95 Å / % possible obs: 100 % / Rmerge(I) obs: 0.247 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1EMA Resolution: 1.9→30 Å / Stereochemistry target values: ENGH & HUBER /
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Refinement step | Cycle: LAST / Resolution: 1.9→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.94 Å
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Refinement | *PLUS Highest resolution: 1.9 Å / Lowest resolution: 6 Å / Num. reflection obs: 54921 / Num. reflection Rfree: 5471 / Rfactor Rfree: 0.226 / Rfactor Rwork: 0.317 | ||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||
Refine LS restraints | *PLUS
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