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Yorodumi- PDB-4zf3: Crystal structure of Green Fluorescent Protein (GFP); S65T, H148D... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4zf3 | ||||||
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Title | Crystal structure of Green Fluorescent Protein (GFP); S65T, H148D; circular permutant ( 50-51) | ||||||
Components | Green fluorescent protein | ||||||
Keywords | FLUORESCENT PROTEIN | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Aequorea victoria (jellyfish) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 Å | ||||||
Authors | Oltrogge, L.M. / Boxer, S.G. | ||||||
Funding support | United States, 1items
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Citation | Journal: Acs Cent.Sci. / Year: 2015 Title: Short Hydrogen Bonds and Proton Delocalization in Green Fluorescent Protein (GFP). Authors: Oltrogge, L.M. / 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 | 4zf3.cif.gz | 98.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4zf3.ent.gz | 73.3 KB | Display | PDB format |
PDBx/mmJSON format | 4zf3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4zf3_validation.pdf.gz | 443.6 KB | Display | wwPDB validaton report |
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Full document | 4zf3_full_validation.pdf.gz | 450.6 KB | Display | |
Data in XML | 4zf3_validation.xml.gz | 18 KB | Display | |
Data in CIF | 4zf3_validation.cif.gz | 23.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zf/4zf3 ftp://data.pdbj.org/pub/pdb/validation_reports/zf/4zf3 | HTTPS FTP |
-Related structure data
Related structure data | 4zf4C 4zf5C 2dufS 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 28176.395 Da / Num. of mol.: 2 Mutation: S30R, Y39I, C48S, F64L, S65T, Q80R, F99S, N105K, E111V, I128Y, Y145F, H148D, M153T, K156N, V163A, K166T, I167V, I171V, S205T, A206V Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aequorea victoria (jellyfish) / Gene: GFP / Plasmid: pET-15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: P42212, UniProt: A0A059PIQ0*PLUS #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 grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5 Details: 50 mM sodium acetate, 100 mM NaCl, 5% (wt/vol) PEG 3550 |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 3, 2014 |
Radiation | Monochromator: Double-crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→37.8 Å / Num. obs: 27729 / % possible obs: 99.3 % / Redundancy: 4.9 % / Biso Wilson estimate: 29.87 Å2 / Rmerge(I) obs: 0.069 / Net I/σ(I): 10.9 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2DUF Resolution: 1.9→34.309 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 28.8 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 73.56 Å2 / Biso mean: 37.8076 Å2 / Biso min: 14.98 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.9→34.309 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10
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