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Open data
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Basic information
Entry | Database: PDB / ID: 2emo | ||||||
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Title | GREEN FLUORESCENT PROTEIN FROM AEQUOREA VICTORIA, MUTANT | ||||||
![]() | GREEN FLUORESCENT PROTEIN | ||||||
![]() | LUMINESCENCE / FLUORESCENT PROTEIN / BETA-BARREL / BIOLUMINESCENCE | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Palm, G. / Zdanov, A. / Wlodawer, A. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 50.3 KB | Display | ![]() |
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PDB format | ![]() | 37.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 435.9 KB | Display | ![]() |
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Full document | ![]() | 448.6 KB | Display | |
Data in XML | ![]() | 12.2 KB | Display | |
Data in CIF | ![]() | 16.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1emcC ![]() 1emeC ![]() 1emfC ![]() 1emkC ![]() 1emlC ![]() 1emmC ![]() 2emdC ![]() 2emnC ![]() 1emaS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Details | THE BIOLOGICALLY ACTIVE MOLECULE IS A DIMER. |
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Components
#1: Protein | Mass: 26918.361 Da / Num. of mol.: 1 / Mutation: INS(A1[B]), F64L, Y66H, V163A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Water | ChemComp-HOH / |
Nonpolymer details | CSH 66: THE CHROMOPHOR |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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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: 21 MG/ML IN 20 MM TRIS/HCL, PH 8.0 WELL SOLUTION: 1.95 M AS, 100 MM TRIS HCL, PH 8.5 PROTEIN:WELL 1:1, vapor diffusion - hanging drop PH range: 8.0-8.5 | |||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / 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: ![]() |
Detector | Type: SIEMENS HI-STAR / Detector: AREA DETECTOR / Date: Jul 15, 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: 2.5→20 Å / Num. obs: 11067 / % possible obs: 78.1 % / Observed criterion σ(I): 0 / Redundancy: 6.9 % / Rsym value: 0.091 / Net I/σ(I): 16.7 |
Reflection shell | Resolution: 2.5→2.59 Å / Mean I/σ(I) obs: 2 / Rsym value: 0.306 / % possible all: 50.5 |
Reflection | *PLUS Rmerge(I) obs: 0.091 |
Reflection shell | *PLUS % possible obs: 50 % / Rmerge(I) obs: 0.306 |
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Processing
Software |
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1EMA Resolution: 2.6→10 Å / Rfactor Rfree error: 0.014 / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / Isotropic thermal model: B-FACTORS SET TO 30.0 / 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). DUE TO LOW QUALITY DATA THE STRUCTURE COULD NOT BE ...Details: PARAMETERS FOR THE CHROMOPHORE WERE ESTIMATED ACCORDING TO A MODEL COMPOUND (B.TINANT ET AL., CRYST. STRUCT. COMM., 1980, 9, 671-674). DUE TO LOW QUALITY DATA THE STRUCTURE COULD NOT BE FULLY REFINED. FOR THE SAME MUTANT, BUT DIFFERENT CRYSTAL FORM SE ENTRY BNL-5139; FOR A VERY SIMILAR MUTANT IN THE SAME SPACE GROUP SEE ENTRY BNL-5144.
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Refinement step | Cycle: LAST / Resolution: 2.6→10 Å
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LS refinement shell | Resolution: 2.6→2.72 Å / Rfactor Rfree error: 0.063 / Total num. of bins used: 8
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Xplor file |
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Software | *PLUS Name: ![]() | ||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
LS refinement shell | *PLUS Rfactor obs: 0.211 |