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Yorodumi- PDB-4rtc: Crystal structure of the green fluorescent variant, nowGFP, of th... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4rtc | ||||||
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Title | Crystal structure of the green fluorescent variant, nowGFP, of the cyan Cerulean at pH 9.0 | ||||||
Components | nowGFP | ||||||
Keywords | FLUORESCENT PROTEIN / nowGFP / Cerulean variant / beta-barrel / TWG chromophore | ||||||
Function / homology | Green Fluorescent Protein / Green fluorescent protein / Beta Barrel / Mainly Beta Function and homology information | ||||||
Biological species | SYNTHETIC (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å | ||||||
Authors | Pletnev, V.Z. / Pletneva, N.V. / Pletnev, S.V. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2015 Title: Structure of the green fluorescent protein NowGFP with an anionic tryptophan-based chromophore. Authors: Pletnev, V.Z. / Pletneva, N.V. / Sarkisyan, K.S. / Mishin, A.S. / Lukyanov, K.A. / Goryacheva, E.A. / Ziganshin, R.H. / Dauter, Z. / Pletnev, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4rtc.cif.gz | 119.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4rtc.ent.gz | 91.7 KB | Display | PDB format |
PDBx/mmJSON format | 4rtc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4rtc_validation.pdf.gz | 450.5 KB | Display | wwPDB validaton report |
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Full document | 4rtc_full_validation.pdf.gz | 457.8 KB | Display | |
Data in XML | 4rtc_validation.xml.gz | 15.1 KB | Display | |
Data in CIF | 4rtc_validation.cif.gz | 22.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rt/4rtc ftp://data.pdbj.org/pub/pdb/validation_reports/rt/4rtc | HTTPS FTP |
-Related structure data
Related structure data | 4rysC 4rywC 2wsoS 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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Details | One monomer in the assymetric unit |
-Components
#1: Protein | Mass: 27873.379 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) SYNTHETIC (others) / Production host: Escherichia coli (E. coli) / Strain (production host): XL1 | ||||
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#2: Chemical | #3: Water | ChemComp-HOH / | Sequence details | THIS PROTEIN IS A GENE-ENGINEERED | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.8 Å3/Da / Density % sol: 56.02 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9 Details: 14mM KH2PO4, pH 4.8, 14% PEG3350, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: 2014 / Details: mirrors | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.35→30 Å / Num. obs: 67619 / % possible obs: 100 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.056 / Net I/σ(I): 10.1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2WSO Resolution: 1.35→27.42 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.957 / Cross valid method: THROUGHOUT / ESU R: 0.048 / ESU R Free: 0.048 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.085 Å2
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Refinement step | Cycle: LAST / Resolution: 1.35→27.42 Å
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Refine LS restraints |
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