+Open data
-Basic information
Entry | Database: PDB / ID: 8iyz | ||||||
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Title | mTurquoise2 S65T | ||||||
Components | Green fluorescent protein | ||||||
Keywords | FLUORESCENT PROTEIN / monomer | ||||||
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: 1.99 Å | ||||||
Authors | Kang, J.S. / Li, S.A. | ||||||
Funding support | China, 1items
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Citation | Journal: To Be Published Title: A unified intracellular pH spectrum with sitepHorin-a quantum-entanglement-based pH-sensitive and ratiometric fluorescent protein Authors: Kang, J.S. / Li, S.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8iyz.cif.gz | 64.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8iyz.ent.gz | 45.3 KB | Display | PDB format |
PDBx/mmJSON format | 8iyz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8iyz_validation.pdf.gz | 424.9 KB | Display | wwPDB validaton report |
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Full document | 8iyz_full_validation.pdf.gz | 425.7 KB | Display | |
Data in XML | 8iyz_validation.xml.gz | 14.2 KB | Display | |
Data in CIF | 8iyz_validation.cif.gz | 19.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/iy/8iyz ftp://data.pdbj.org/pub/pdb/validation_reports/iy/8iyz | HTTPS FTP |
-Related structure data
Related structure data | 8iyyC 8iz0C 8iz1C 8iz2C 8iz3C C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 27772.305 Da / Num. of mol.: 1 Mutation: F64L, S65T, Y66W, S72A, N146F, H148D, M153T, V163A, S175G, A206K, H231L Source method: isolated from a genetically manipulated source Details: Author stated: The SITE-pHorin is the cyan fluorescence protein mTurquoise2 mutant. The mTurquoise2 was firstly designed in the paper (DOI: 10.1038/ncomms1738, PDB ID: 3ztf) Source: (gene. exp.) Aequorea victoria (jellyfish) / Gene: GFP / Production host: Escherichia coli (E. coli) / References: UniProt: P42212 |
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#2: Water | ChemComp-HOH / |
Has ligand of interest | Y |
Has protein modification | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.17 Å3/Da / Density % sol: 39.24 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 20% PEG 8000, 100 mM MgCl2, 100 mM HEPES PH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.979 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 5, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.99→50 Å / Num. obs: 15931 / % possible obs: 99.9 % / Redundancy: 10.5 % / Rmerge(I) obs: 0.23 / Rpim(I) all: 0.071 / Net I/σ(I): 11.5 |
Reflection shell | Resolution: 2→2.03 Å / Redundancy: 6 % / Rmerge(I) obs: 0.678 / Mean I/σ(I) obs: 1.67 / Num. unique obs: 510 / Rpim(I) all: 0.29 / % possible all: 99.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.99→35.25 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 19.33 / 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: 1.99→35.25 Å
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Refine LS restraints |
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LS refinement shell |
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