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Yorodumi- PDB-7km4: Crystal Structure of Oxidized Version of Redox-Sensitive Superfol... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7km4 | ||||||
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Title | Crystal Structure of Oxidized Version of Redox-Sensitive Superfolder Green Fluorescent Protein | ||||||
Components | Green fluorescent protein | ||||||
Keywords | FLUORESCENT PROTEIN / Redox Sensitive / GFP | ||||||
Function / homology | Green fluorescent protein, GFP / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / bioluminescence / generation of precursor metabolites and energy / Green fluorescent protein Function and homology information | ||||||
Biological species | Aequorea victoria (jellyfish) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å | ||||||
Authors | Nguyen, T. / Nicely, N.I. / McCafferty, D.G. | ||||||
Funding support | United States, 1items
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Citation | Journal: To be Published Title: Crystal Structure of Oxidized Version of Redox-Sensitive Superfolder Green Fluorescent Protein Authors: Nguyen, T. / Nicely, N.I. / McCafferty, D.G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7km4.cif.gz | 67.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7km4.ent.gz | 40.6 KB | Display | PDB format |
PDBx/mmJSON format | 7km4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/km/7km4 ftp://data.pdbj.org/pub/pdb/validation_reports/km/7km4 | 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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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 27845.365 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aequorea victoria (jellyfish) / Gene: GFP / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P42212 |
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#2: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.12 Å3/Da / Density % sol: 42.03 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / Details: 200, Potassium Chloride, 20% PEG-3350 / Temp details: Room Temperature |
-Data collection
Diffraction | Mean temperature: 298 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 10, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.65→50 Å / Num. obs: 7433 / % possible obs: 100 % / Redundancy: 10.3 % / Biso Wilson estimate: 56.56 Å2 / Rpim(I) all: 0.031 / Rsym value: 0.059 / Net I/σ(I): 3.3 |
Reflection shell | Resolution: 2.65→2.7 Å / Redundancy: 10.3 % / Num. unique obs: 1426 / Rpim(I) all: 0.249 / Rsym value: 0.808 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2B3P Resolution: 2.65→40.43 Å / SU ML: 0.3792 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 32.2407 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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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 mean: 57.42 Å2 | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.65→40.43 Å
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Refine LS restraints |
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LS refinement shell |
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