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Yorodumi- PDB-6ofk: Crystal structure of green fluorescent protein (GFP); S65T; ih ci... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6ofk | |||||||||
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Title | Crystal structure of green fluorescent protein (GFP); S65T; ih circular permutant (50-51) | |||||||||
Components | Green Fluorescent Protein (GFP); S65T; ih circular permutant (50-51) | |||||||||
Keywords | FLUORESCENT PROTEIN / GFP | |||||||||
Function / homology | Function and homology information serine-type endopeptidase inhibitor activity / extracellular space / metal ion binding Similarity search - Function | |||||||||
Biological species | Aequorea victoria (jellyfish) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.15 Å | |||||||||
Authors | Lin, C.-Y. / Romei, M.G. / Mathews, I.I. / Boxer, S.G. | |||||||||
Funding support | United States, 1items
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Citation | Journal: J.Am.Chem.Soc. / Year: 2019 Title: Unified Model for Photophysical and Electro-Optical Properties of Green Fluorescent Proteins. Authors: Lin, C.Y. / Romei, M.G. / Oltrogge, L.M. / Mathews, I.I. / Boxer, S.G. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6ofk.cif.gz | 217.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ofk.ent.gz | 172.2 KB | Display | PDB format |
PDBx/mmJSON format | 6ofk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6ofk_validation.pdf.gz | 453.4 KB | Display | wwPDB validaton report |
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Full document | 6ofk_full_validation.pdf.gz | 459.3 KB | Display | |
Data in XML | 6ofk_validation.xml.gz | 23.6 KB | Display | |
Data in CIF | 6ofk_validation.cif.gz | 34.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/of/6ofk ftp://data.pdbj.org/pub/pdb/validation_reports/of/6ofk | HTTPS FTP |
-Related structure data
Related structure data | 6oflC 6ofmC 6ofnC 6ofoC 4zf3S 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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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
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-Components
#1: Protein | Mass: 28083.334 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aequorea victoria (jellyfish) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P42212*PLUS #2: Chemical | ChemComp-ACT / | #3: 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: 1.91 Å3/Da / Density % sol: 35.51 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / Details: 0.15 M ammonium acetate, 34% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.8856 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 4, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8856 Å / Relative weight: 1 |
Reflection | Resolution: 1.15→36.49 Å / Num. obs: 146731 / % possible obs: 98 % / Redundancy: 13.5 % / Biso Wilson estimate: 15.2 Å2 / CC1/2: 1 / Rrim(I) all: 0.035 / Net I/σ(I): 28.4 |
Reflection shell | Resolution: 1.15→1.19 Å / Redundancy: 12.2 % / Mean I/σ(I) obs: 1.4 / Num. unique obs: 14174 / CC1/2: 0.781 / Rrim(I) all: 1.76 / % possible all: 95.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4zf3 Resolution: 1.15→36.49 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.975 / SU B: 1.659 / SU ML: 0.032 / Cross valid method: THROUGHOUT / ESU R: 0.036 / ESU R Free: 0.036 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.365 Å2
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Refinement step | Cycle: LAST / Resolution: 1.15→36.49 Å
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Refine LS restraints |
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