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Yorodumi- PDB-1qxt: Crystal structure of precyclized intermediate for the green fluor... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1qxt | ||||||
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Title | Crystal structure of precyclized intermediate for the green fluorescent protein R96A variant (A) | ||||||
Components | green-fluorescent protein | ||||||
Keywords | LUMINESCENT PROTEIN / beta barrel / trapped intermediate / chromophore | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Aequorea victoria (jellyfish) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Barondeau, D.P. / Putnam, C.D. / Kassmann, C.J. / Tainer, J.A. / Getzoff, E.D. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1qxt.cif.gz | 59.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1qxt.ent.gz | 42.6 KB | Display | PDB format |
PDBx/mmJSON format | 1qxt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qx/1qxt ftp://data.pdbj.org/pub/pdb/validation_reports/qx/1qxt | HTTPS FTP |
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-Related structure data
Related structure data | 1qy3C 1qyfC 1qyoC 1qyqC 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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-Components
#1: Protein | Mass: 25691.842 Da / Num. of mol.: 1 / Fragment: residues 1-229 / Mutation: R96A F99S M153T V163A F64L S65T Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aequorea victoria (jellyfish) / Gene: GFP / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / 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: 2.17 Å3/Da / Density % sol: 43.36 % | |||||||||||||||||||||||||||||||||||
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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 | |||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging dropDetails: used microseeding., Barondeau, D.P., (2002) J.Am.Chem.Soc., 124, 3522. | |||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.78 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 29, 1999 |
Radiation | Monochromator: CURVED CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.78 Å / Relative weight: 1 |
Reflection | Resolution: 2→20 Å / Num. all: 15708 / Num. obs: 15550 / % possible obs: 99 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 3.53 % / Biso Wilson estimate: 13.8 Å2 / Rsym value: 0.066 / Net I/σ(I): 18.2 |
Reflection shell | Resolution: 2→2.07 Å / Mean I/σ(I) obs: 3.3 / Rsym value: 0.372 / % possible all: 99.8 |
Reflection | *PLUS Highest resolution: 2 Å / Num. measured all: 54856 / Rmerge(I) obs: 0.066 |
Reflection shell | *PLUS % possible obs: 99.8 % / Rmerge(I) obs: 0.372 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1ema Resolution: 2→19.74 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 606673.23 / Data cutoff high rms absF: 606673.23 / 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: 26.5548 Å2 / ksol: 0.385569 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2→19.74 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.13 Å / Rfactor Rfree error: 0.032 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Lowest resolution: 20 Å / Rfactor Rfree: 0.258 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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