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Yorodumi- PDB-2hcg: Structure of S65T Y66F GFP variant after cyclization, carbon-carb... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2hcg | ||||||
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Title | Structure of S65T Y66F GFP variant after cyclization, carbon-carbon bond cleavage, and oxygen incorporation reactions | ||||||
Components | Green fluorescent protein | ||||||
Keywords | LUMINESCENT PROTEIN / post-translational modification / cyclization / cleavage / fluorophore | ||||||
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: J.Am.Chem.Soc. / Year: 2007 Title: The Case of the Missing Ring: Radical Cleavage of a Carbon-Carbon Bond and Implications for GFP Chromophore Biosynthesis Authors: Barondeau, D.P. / 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 | 2hcg.cif.gz | 71.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2hcg.ent.gz | 50.2 KB | Display | PDB format |
PDBx/mmJSON format | 2hcg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hc/2hcg ftp://data.pdbj.org/pub/pdb/validation_reports/hc/2hcg | HTTPS FTP |
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-Related structure data
Related structure data | 2hfcC 2hgdC 2hgyC 1emaS 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: 26763.029 Da / Num. of mol.: 1 / Mutation: F64L, S65T, Y66F, F99S, M153T, V163A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aequorea victoria (jellyfish) / Gene: GFP / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)RIL / References: UniProt: P42212 |
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#2: Chemical | ChemComp-MG / |
#3: Water | ChemComp-HOH / |
Sequence details | RESIDUES THR 65, PHE 66 AND GLY 67 CONSTITUTE THE CHROMOPHORE C99. RESIDUE AT POSITION 65 IS S65T ...RESIDUES THR 65, PHE 66 AND GLY 67 CONSTITUTE |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.11 Å3/Da / Density % sol: 41.8 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 19% PEG 4K, 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: BL9-1 / Wavelength: 0.9706 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Dec 7, 2001 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9706 Å / Relative weight: 1 |
Reflection | Resolution: 1.35→31 Å / Num. obs: 50300 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Biso Wilson estimate: 11.6 Å2 / Rsym value: 0.043 / Net I/σ(I): 26.2 |
Reflection shell | Resolution: 1.35→1.4 Å / Rmerge(I) obs: 0.352 / Mean I/σ(I) obs: 3.1 / Num. unique all: 4869 / % possible all: 97.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1ema Resolution: 1.35→31 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 1.35→31 Å
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Refine LS restraints |
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