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Yorodumi- PDB-4gob: Low pH Crystal Structure of a reconstructed Kaede-type Red Fluore... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4gob | |||||||||
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Title | Low pH Crystal Structure of a reconstructed Kaede-type Red Fluorescent Protein, Least Evolved Ancestor (LEA) | |||||||||
Components | Kaede-type Fluorescent Protein | |||||||||
Keywords | FLUORESCENT PROTEIN / Beta-Barrel / Luminescent Protein | |||||||||
Function / homology | Green Fluorescent Protein / Green fluorescent protein / Beta Barrel / Mainly Beta Function and homology information | |||||||||
Biological species | synthetic construct (others) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.53 Å | |||||||||
Authors | Kim, H. / Grunkemeyer, T.J. / Chen, L. / Fromme, R. / Wachter, R.M. | |||||||||
Citation | Journal: Biochemistry / Year: 2013 Title: Acid-base catalysis and crystal structures of a least evolved ancestral GFP-like protein undergoing green-to-red photoconversion. Authors: Kim, H. / Grunkemeyer, T.J. / Modi, C. / Chen, L. / Fromme, R. / Matz, M.V. / Wachter, R.M. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4gob.cif.gz | 373.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4gob.ent.gz | 305.9 KB | Display | PDB format |
PDBx/mmJSON format | 4gob.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4gob_validation.pdf.gz | 455.4 KB | Display | wwPDB validaton report |
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Full document | 4gob_full_validation.pdf.gz | 467.5 KB | Display | |
Data in XML | 4gob_validation.xml.gz | 36 KB | Display | |
Data in CIF | 4gob_validation.cif.gz | 49.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/go/4gob ftp://data.pdbj.org/pub/pdb/validation_reports/go/4gob | HTTPS FTP |
-Related 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: 26434.064 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Plasmid: pGEM-T / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) #2: 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: 2.36 Å3/Da / Density % sol: 47.87 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 3.8 Details: 20% PEG 4000, 0.12M mM Glycine-phosphate, 100 mM magnesium chloride, pH 3.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9792 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 14, 2012 |
Radiation | Monochromator: Rosenbaum-Rock high-resolution double-crystal Si 111 Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 1.53→50 Å / Num. all: 264165 / Num. obs: 165103 / % possible obs: 94.1 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.042 / Net I/σ(I): 22.5 |
Reflection shell | Resolution: 1.53→1.56 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.465 / Mean I/σ(I) obs: 2.2 / % possible all: 98.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.53→33.98 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.928 / SU B: 3.59 / SU ML: 0.059 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.093 / ESU R Free: 0.087 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES 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: 23.595 Å2
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Refinement step | Cycle: LAST / Resolution: 1.53→33.98 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.53→1.57 Å / Total num. of bins used: 20
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