+Open data
-Basic information
Entry | Database: PDB / ID: 4lw5 | ||||||
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Title | Crystal structure of all-trans green fluorescent protein | ||||||
Components | Green fluorescent protein | ||||||
Keywords | FLUORESCENT PROTEIN / 11-stranded beta barrel | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Aequorea victoria (jellyfish) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.55 Å | ||||||
Authors | Rosenman, D.J. / Huang, Y.-M. / Xia, K. / Vanroey, P. / Colon, W. / Bystroff, C. | ||||||
Citation | Journal: Protein Sci. / Year: 2014 Title: Green-lighting green fluorescent protein: Faster and more efficient folding by eliminating a cis-trans peptide isomerization event. Authors: Rosenman, D.J. / Huang, Y.M. / Xia, K. / Fraser, K. / Jones, V.E. / Lamberson, C.M. / Van Roey, P. / Colon, W. / Bystroff, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4lw5.cif.gz | 237.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4lw5.ent.gz | 191.3 KB | Display | PDB format |
PDBx/mmJSON format | 4lw5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lw/4lw5 ftp://data.pdbj.org/pub/pdb/validation_reports/lw/4lw5 | HTTPS FTP |
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-Related structure data
Related structure data | 2b3pS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 26940.346 Da / Num. of mol.: 5 / Fragment: SEE REMARK 999 / Mutation: yes Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aequorea victoria (jellyfish) / Gene: GFP / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P42212 #2: Water | ChemComp-HOH / | Sequence details | THE FLUOROPHORE (CRO) IS GENERATED BY AN AUTOCATALYTIC CYCLIZATION OF THE POLYPEPTIDE BACKBONE ...THE FLUOROPHOR | |
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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: 2.26 Å3/Da / Density % sol: 45.5 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.1 M sodium chloride, 0.1 M HEPES, pH 7.5, 20% w/v PEG8000, VAPOR DIFFUSION, SITTING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X4C / Wavelength: 0.97907 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Oct 12, 2011 |
Radiation | Monochromator: Bent single crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97907 Å / Relative weight: 1 |
Reflection | Resolution: 2.55→33.826 Å / Num. all: 40443 / Num. obs: 40237 / % possible obs: 99.49 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 6.9 % / Biso Wilson estimate: 27.5 Å2 / Rsym value: 0.119 / Net I/σ(I): 20.2 |
Reflection shell | Resolution: 2.55→2.71 Å / Redundancy: 7 % / Mean I/σ(I) obs: 3.13 / Rsym value: 0.536 / % possible all: 100 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2B3P Resolution: 2.55→19.94 Å / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Bsol: 25.1599 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 85.48 Å2 / Biso mean: 35.25 Å2 / Biso min: 7.77 Å2
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Refinement step | Cycle: LAST / Resolution: 2.55→19.94 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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Xplor file |
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