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Yorodumi- PDB-4jeo: Crystal structure of red fluorescent protein lanRFPdam exposed to... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4jeo | ||||||
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Title | Crystal structure of red fluorescent protein lanRFPdam exposed to prolonged X-ray irradiation | ||||||
Components | Red fluorescent protein blFP-R5 | ||||||
Keywords | FLUORESCENT PROTEIN / lanRFP / red fluorescent protein / beta-barrel / Gly-Tyr-Gly chromophore / cephalochordate | ||||||
Function / homology | Green fluorescent protein-related / Green fluorescent protein / bioluminescence / Green Fluorescent Protein / Green fluorescent protein / Green fluorescent protein / Beta Barrel / Mainly Beta / Red fluorescent protein blFP-R5 Function and homology information | ||||||
Biological species | Branchiostoma lanceolatum (amphioxus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å | ||||||
Authors | Pletnev, V.Z. / Pletneva, N.V. / Pletnev, S.V. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2013 Title: Structure of the red fluorescent protein from a lancelet (Branchiostoma lanceolatum): a novel GYG chromophore covalently bound to a nearby tyrosine. Authors: Pletnev, V.Z. / Pletneva, N.V. / Lukyanov, K.A. / Souslova, E.A. / Fradkov, A.F. / Chudakov, D.M. / Chepurnykh, T. / Yampolsky, I.V. / Wlodawer, A. / 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 | 4jeo.cif.gz | 109.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4jeo.ent.gz | 83.1 KB | Display | PDB format |
PDBx/mmJSON format | 4jeo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4jeo_validation.pdf.gz | 447.4 KB | Display | wwPDB validaton report |
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Full document | 4jeo_full_validation.pdf.gz | 451.1 KB | Display | |
Data in XML | 4jeo_validation.xml.gz | 22.1 KB | Display | |
Data in CIF | 4jeo_validation.cif.gz | 31.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/je/4jeo ftp://data.pdbj.org/pub/pdb/validation_reports/je/4jeo | HTTPS FTP |
-Related structure data
Related structure data | 4hvfSC 4jf9C 4jgeC 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 25791.004 Da / Num. of mol.: 2 / Mutation: M1S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Branchiostoma lanceolatum (amphioxus) / Gene: blFP-R5 / Plasmid: pQE30 / Production host: Escherichia coli (E. coli) / References: UniProt: B1PND0 #2: Chemical | ChemComp-GOL / | #3: Water | ChemComp-HOH / | |
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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: 3.96 Å3/Da / Density % sol: 68.91 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 9 mg/ml of lanRFP in 20 mM Tris pH 8.0, 200 mM NaCl, 5 mM EDTA mixed with an equal amount of reservoir solution - 1M Na-citrate, 0.1M Tris pH 7.0 , 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 / 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: 2.34→30 Å / Num. all: 31762 / Num. obs: 35065 / % possible obs: 98.7 % / Redundancy: 5.6 % / Rmerge(I) obs: 0.131 / Χ2: 0.971 / Net I/σ(I): 7.2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4HVF Resolution: 2.35→29.83 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.931 / WRfactor Rfree: 0.1841 / WRfactor Rwork: 0.1406 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.898 / SU R Cruickshank DPI: 0.1777 / SU Rfree: 0.1683 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.178 / ESU R Free: 0.168 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 65.48 Å2 / Biso mean: 19.2455 Å2 / Biso min: 3.06 Å2
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Refinement step | Cycle: LAST / Resolution: 2.35→29.83 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.346→2.407 Å / Total num. of bins used: 20
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