+Open data
-Basic information
Entry | Database: PDB / ID: 7cd8 | |||||||||
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Title | GFP-40/GFPuv complex, Form II | |||||||||
Components |
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Keywords | PROTEIN BINDING / Synthetic binding protein | |||||||||
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) synthetic construct (others) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | |||||||||
Authors | Yasui, N. / Yamashita, A. | |||||||||
Funding support | Japan, 2items
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Citation | Journal: J.Biochem. / Year: 2021 Title: A sweet protein monellin as a non-antibody scaffold for synthetic binding proteins. Authors: Yasui, N. / Nakamura, K. / Yamashita, A. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7cd8.cif.gz | 89.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7cd8.ent.gz | 64.6 KB | Display | PDB format |
PDBx/mmJSON format | 7cd8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7cd8_validation.pdf.gz | 425.5 KB | Display | wwPDB validaton report |
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Full document | 7cd8_full_validation.pdf.gz | 426.9 KB | Display | |
Data in XML | 7cd8_validation.xml.gz | 17.5 KB | Display | |
Data in CIF | 7cd8_validation.cif.gz | 25.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cd/7cd8 ftp://data.pdbj.org/pub/pdb/validation_reports/cd/7cd8 | HTTPS FTP |
-Related structure data
Related structure data | 7cd7C 1b9cS 2o9uS 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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Unit cell |
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-Components
#1: Protein | Mass: 26811.100 Da / Num. of mol.: 1 / Fragment: UNP residues 3-238 / Mutation: Q80R, F99S, M153T, V163A, A206K 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: Protein | Mass: 11554.108 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) |
#3: 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: 2.64 Å3/Da / Density % sol: 53.42 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 5.5% (w/v) PEG 8000, 5% (v/v) ethylene glycol, 50 mM [Co(NH3)6]Cl3, 0.1 M HEPES-Na, pH 7.5 |
-Data collection
Diffraction | Mean temperature: 93 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 17, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. obs: 28608 / % possible obs: 100 % / Redundancy: 6 % / CC1/2: 0.998 / Rsym value: 0.074 / Net I/σ(I): 22.3 |
Reflection shell | Resolution: 2→2.03 Å / Mean I/σ(I) obs: 2.7 / Num. unique obs: 1403 / CC1/2: 0.911 / Rsym value: 0.476 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1B9C, 2O9U Resolution: 2→46.981 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 21.78 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→46.981 Å
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Refine LS restraints |
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LS refinement shell |
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