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- PDB-1qyo: Anaerobic precylization intermediate crystal structure for S65G Y... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1qyo | ||||||
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Title | Anaerobic precylization intermediate crystal structure for S65G Y66G GFP variant | ||||||
![]() | green-fluorescent protein | ||||||
![]() | LUMINESCENT PROTEIN / beta barrel / chromophore / trapped intermediate | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Barondeau, D.P. / Putnam, C.D. / Kassmann, C.J. / Tainer, J.A. / Getzoff, E.D. | ||||||
![]() | ![]() Title: Mechanism and energetics of green fluorescent protein chromophore synthesis revealed by trapped intermediate structures. Authors: Barondeau, D.P. / Putnam, C.D. / Kassmann, C.J. / Tainer, J.A. / Getzoff, E.D. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 65.5 KB | Display | ![]() |
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PDB format | ![]() | 47.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 416.2 KB | Display | ![]() |
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Full document | ![]() | 416.4 KB | Display | |
Data in XML | ![]() | 13.1 KB | Display | |
Data in CIF | ![]() | 19.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1qxtC ![]() 1qy3C ![]() 1qyfC ![]() 1qyqC ![]() 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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Unit cell |
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Components
#1: Protein | Mass: 26633.918 Da / Num. of mol.: 1 / Mutation: F99S, M153T, V163A, F64L, S65G, Y66G Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.15 Å3/Da / Density % sol: 42.81 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8 Details: PEG 4000, Magnesium Chloride, Hepes, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 2, 2002 |
Radiation | Monochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54179 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→20 Å / Num. all: 21947 / Num. obs: 21270 / % possible obs: 96.5 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Biso Wilson estimate: 13.2 Å2 / Rsym value: 0.072 / Net I/σ(I): 20.2 |
Reflection shell | Resolution: 1.8→1.86 Å / Mean I/σ(I) obs: 3.4 / Rsym value: 0.366 / % possible all: 85.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1ema Resolution: 1.8→17.44 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 493845.43 / Data cutoff high rms absF: 493845.43 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 20.5896 Å2 / ksol: 0.35782 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.8→17.44 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.91 Å / Rfactor Rfree error: 0.028 / Total num. of bins used: 6
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Xplor file |
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