+Open data
-Basic information
Entry | Database: PDB / ID: 2dd7 | ||||||
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Title | A GFP-like protein from marine copepod, Chiridius poppei | ||||||
Components | green fluorescent protein | ||||||
Keywords | LUMINESCENT PROTEIN / FLUORESCENT PROTEIN | ||||||
Function / homology | Green fluorescent protein-related / Green fluorescent protein / bioluminescence / Green Fluorescent Protein / Green fluorescent protein / Green fluorescent protein / Beta Barrel / Mainly Beta / Green fluorescent protein Function and homology information | ||||||
Biological species | Chiridius poppei (crustacean) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Suto, K. / Masuda, H. / Takenaka, Y. / Mizuno, H. | ||||||
Citation | Journal: Genes Cells / Year: 2009 Title: Structural basis for red-shifted emission of a GFP-like protein from the marine copepod Chiridius poppei Authors: Suto, K. / Masuda, H. / Takenaka, Y. / Tsuji, F.I. / Mizuno, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2dd7.cif.gz | 103.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2dd7.ent.gz | 84.6 KB | Display | PDB format |
PDBx/mmJSON format | 2dd7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2dd7_validation.pdf.gz | 459.1 KB | Display | wwPDB validaton report |
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Full document | 2dd7_full_validation.pdf.gz | 467.3 KB | Display | |
Data in XML | 2dd7_validation.xml.gz | 23.7 KB | Display | |
Data in CIF | 2dd7_validation.cif.gz | 34.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dd/2dd7 ftp://data.pdbj.org/pub/pdb/validation_reports/dd/2dd7 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 24620.863 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Chiridius poppei (crustacean) / Plasmid: pET-101 / Production host: Escherichia coli (E. coli) / References: UniProt: Q2MHN7 #2: Chemical | ChemComp-CL / | #3: Chemical | ChemComp-CXS / | #4: Water | ChemComp-HOH / | Sequence details | GLY 55, TYR 56 AND GLY 57 ARE MODIFIED TO MAKE CHROMOPHOR | |
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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: 4.18 Å3/Da / Density % sol: 70.59 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 10.5 Details: 0.1M CAPS (pH 10.5), 2.2M Ammonium Sulfate, 0.2M NaCl, VAPOR DIFFUSION, SITTING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 0.97986 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 1, 2004 |
Radiation | Monochromator: SILICON (1 1 1) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97986 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→30 Å / Num. obs: 65109 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / Biso Wilson estimate: 9.9 Å2 |
Reflection shell | Resolution: 1.9→2 Å / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→28.82 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 3445681.75 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 47.9488 Å2 / ksol: 0.393849 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.9→28.82 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→2.02 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 6
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Xplor file |
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