+Open data
-Basic information
Entry | Database: PDB / ID: 3gex | ||||||
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Title | 1.6 angstrom crystal structure of fluorescent protein Cypet | ||||||
Components | Green fluorescent protein | ||||||
Keywords | FLUORESCENT PROTEIN / BETA BARREL / CHROMOPHORE / Luminescence / Photoprotein | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Aequorea victoria (jellyfish) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||
Authors | Hu, X. / Liu, R. | ||||||
Citation | Journal: To be Published Title: 1.6 angstrom crystal structure of fluorescent protein Cypet Authors: Liu, R. / Ding, Y. / Hu, X. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3gex.cif.gz | 65.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3gex.ent.gz | 47.1 KB | Display | PDB format |
PDBx/mmJSON format | 3gex.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ge/3gex ftp://data.pdbj.org/pub/pdb/validation_reports/ge/3gex | HTTPS FTP |
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-Related structure data
Related structure data | 1qyoS S: Starting model for refinement |
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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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Details | AUTHOR STATES THAT THE BIOLOGICAL UNIT IS UNKNOWN. |
-Components
#1: Protein | Mass: 27496.031 Da / Num. of mol.: 1 / Mutation: T10G, V12I, D20E, A88V, I168A, E173T, L195I Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aequorea victoria (jellyfish) / Gene: GFP / Plasmid: pT7His-CyPet / Production host: Escherichia coli (E. coli) / References: UniProt: P42212 |
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#2: Water | ChemComp-HOH / |
Sequence details | THE SEQUENCE WAS MUTATED FROM SER & TYR TO THR & TRP, RESPECTIVELY, TO FORM CHROMOPHORE. THESE FIVE ...THE SEQUENCE WAS MUTATED FROM SER & TYR TO THR & TRP, RESPECTIVE |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.08 Å3/Da / Density % sol: 40.99 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 30% PEG 4000, 0.1M Tris-HCl pH 8.5, 0.2M Lithium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Dec 5, 2008 |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→50 Å / Num. all: 31080 / Num. obs: 28302 / % possible obs: 91.1 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 2.3 % / Rsym value: 0.039 / Net I/σ(I): 16.7 |
Reflection shell | Resolution: 1.6→1.66 Å / Redundancy: 1.8 % / Mean I/σ(I) obs: 3.2 / Num. unique all: 1825 / Rsym value: 0.23 / % possible all: 59.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1QYO Resolution: 1.6→20.41 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.948 / SU B: 1.771 / SU ML: 0.064 / Cross valid method: THROUGHOUT / ESU R: 0.115 / ESU R Free: 0.112 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.199 Å2
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Refinement step | Cycle: LAST / Resolution: 1.6→20.41 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.6→1.641 Å / Total num. of bins used: 20
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