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Open data
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Basic information
Entry | Database: PDB / ID: 2emd | |||||||||
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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 | ![]() | 57.7 KB | Display | ![]() |
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PDB format | ![]() | 45.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 435.9 KB | Display | ![]() |
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Full document | ![]() | 437.8 KB | Display | |
Data in XML | ![]() | 12.1 KB | Display | |
Data in CIF | ![]() | 16.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1emcC ![]() 1emeC ![]() 1emfC ![]() 1emkC ![]() 1emlC ![]() 1emmC ![]() 2emnC ![]() 2emoC ![]() 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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Components on special symmetry positions |
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Details | THE BIOLOGICALLY ACTIVE MOLECULE IS A DIMER. |
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Components
#1: Protein | Mass: 26946.414 Da / Num. of mol.: 1 / Mutation: INS(A1[B]), F64L, Y66H 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: 4.2 Å3/Da / Density % sol: 71 % | |||||||||||||||||||||||||
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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 WELL SOLUTION: 2.1 M AS, 100 MM TRIS/HCL, 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: ![]() |
Detector | Type: MACSCIENCE / Detector: IMAGE PLATE / Date: Jun 25, 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→10 Å / Num. obs: 25953 / % possible obs: 82.8 % / Observed criterion σ(I): 2 / Redundancy: 5.6 % / Rsym value: 0.096 / Net I/σ(I): 15.6 |
Reflection shell | Resolution: 2→2.07 Å / Mean I/σ(I) obs: 2.9 / Rsym value: 0.231 / % possible all: 46.9 |
Reflection | *PLUS Rmerge(I) obs: 0.056 |
Reflection shell | *PLUS % possible obs: 46.9 % / Rmerge(I) obs: 0.231 |
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Processing
Software |
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1EMA Resolution: 2→10 Å / Rfactor Rfree error: 0.0055 / 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)
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Displacement parameters | Biso mean: 22.4 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→10 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: RESTRAINTS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2→2.09 Å / Rfactor Rfree error: 0.027 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor obs: 0.294 |