+Open data
-Basic information
Entry | Database: PDB / ID: 1emk | ||||||
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Title | GREEN FLUORESCENT PROTEIN FROM AEQUOREA VICTORIA, MUTANT | ||||||
Components | GREEN FLUORESCENT PROTEIN | ||||||
Keywords | LUMINESCENCE / FLUORESCENT PROTEIN / BETA-BARREL / BIOLUMINESCENCE | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Aequorea victoria (jellyfish) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Palm, G. / Zdanov, A. / Wlodawer, A. | ||||||
Citation | Journal: Nat.Struct.Biol. / Year: 1997 Title: The structural basis for spectral variations in green fluorescent protein. Authors: Palm, G.J. / Zdanov, A. / Gaitanaris, G.A. / Stauber, R. / Pavlakis, G.N. / Wlodawer, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1emk.cif.gz | 57 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1emk.ent.gz | 44.2 KB | Display | PDB format |
PDBx/mmJSON format | 1emk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1emk_validation.pdf.gz | 436.6 KB | Display | wwPDB validaton report |
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Full document | 1emk_full_validation.pdf.gz | 443.2 KB | Display | |
Data in XML | 1emk_validation.xml.gz | 12.6 KB | Display | |
Data in CIF | 1emk_validation.cif.gz | 17.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/em/1emk ftp://data.pdbj.org/pub/pdb/validation_reports/em/1emk | HTTPS FTP |
-Related structure data
Related structure data | 1emcC 1emeC 1emfC 1emlC 1emmC 2emdC 2emnC 2emoC 1emaS C: citing same article (ref.) S: Starting model for refinement |
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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 | THE AUTHOR NOTES THAT THE BIOLOGICALLY ACTIVE MOLECULE IS A DIMER. |
-Components
#1: Protein | Mass: 26961.381 Da / Num. of mol.: 1 / Mutation: INS(A1[B]), F64L, S65C, I167T, K238N Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aequorea victoria (jellyfish) / Tissue: CIRCUMORAL RING CANAL / Gene: GFP / Organ: PHOTOGENIC ORGAN / Plasmid: PFRED25 / Cellular location (production host): CYTOPLASM / Gene (production host): SG25 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21, OMEGA876 / References: UniProt: P42212 |
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#2: Water | ChemComp-HOH / |
-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: 57 % | |||||||||||||||||||||||||
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 8.5 Details: PROTEIN WAS CRYSTALLIZED BY HANGING DROP METHOD. PROTEIN SOLUTION: 17 MG/ML IN 20 MM TRISCL WELL SOLUTION: 1.95 M AS, 100MM TRISCL, PH 8.5 PROTEIN:WELL 1:1, vapor diffusion - hanging drop | |||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging dropDetails: protein solution is mixed in a 1:1 ratio with well solution | |||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 295 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Jun 27, 1996 / Details: MIRROR |
Radiation | Monochromator: NI / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→10 Å / Num. obs: 16826 / % possible obs: 96.3 % / Observed criterion σ(I): 1 / Redundancy: 5.2 % / Rmerge(I) obs: 0.093 / Rsym value: 0.093 |
Reflection shell | Resolution: 2.1→2.19 Å / Rsym value: 0.334 / % possible all: 92.7 |
Reflection shell | *PLUS % possible obs: 92.7 % / Rmerge(I) obs: 0.334 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1EMA Resolution: 2.1→10 Å / Rfactor Rfree error: 0.0087 / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 Details: PARAMETERS FOR THE CHROMOPHORE WERE ESTIMATED ACCORDING TO A MODEL COMPOUND (B.TINANT ET AL., CRYST. STRUCT. COMM., 1980, 9, 671-674). SG OF CCY 66 WAS REFINED IN TWO ALTERNATE CONFORMATIONS.
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Displacement parameters | Biso mean: 33.7 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→10 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.19 Å / Rfactor Rfree error: 0.042 / Total num. of bins used: 8
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | *PLUS Rfactor obs: 0.31 |