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Yorodumi- PDB-1rmm: Probing the Role of Tryptophans in Aequorea Victoria Green Fluore... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1rmm | ||||||
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Title | Probing the Role of Tryptophans in Aequorea Victoria Green Fluorescent Proteins with an Expanded Genetic Code | ||||||
Components | SIGF1-GFP fusion protein | ||||||
Keywords | LUMINESCENT PROTEIN / Beta-barrel / GFP / Noncanonical amino acid | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Aequorea victoria (jellyfish) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Budisa, N. / Pal, P.P. / Alefelder, S. / Birle, P. / Krywcun, T. / Rubini, M. / Wenger, W. / Bae, J.H. / Steiner, T. | ||||||
Citation | Journal: Biol.Chem. / Year: 2004 Title: Probing the role of tryptophans in Aequorea victoria green fluorescent proteins with an expanded genetic code Authors: Budisa, N. / Pal, P.P. / Alefelder, S. / Birle, P. / Krywcun, T. / Rubini, M. / Wenger, W. / Bae, J.H. / Steiner, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1rmm.cif.gz | 58.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1rmm.ent.gz | 41.8 KB | Display | PDB format |
PDBx/mmJSON format | 1rmm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rm/1rmm ftp://data.pdbj.org/pub/pdb/validation_reports/rm/1rmm | HTTPS FTP |
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-Related structure data
Related structure data | 1rm9C 1rmoC 1rmpC 1emgS S: Starting model for refinement C: citing same article (ref.) |
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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: 25726.816 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aequorea victoria (jellyfish) / Plasmid details: plasmid bought from BD Clontech / Plasmid: pECFP / Production host: Escherichia coli (E. coli) / 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: 2.2 Å3/Da / Density % sol: 44.06 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 14% PEG 1000, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 9, 2001 |
Radiation | Monochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→500 Å / Num. all: 18469 / Num. obs: 17746 / % possible obs: 95.9 % / Observed criterion σ(I): 2 / Biso Wilson estimate: 26.7 Å2 |
Reflection shell | Resolution: 1.9→1.97 Å / % possible all: 82.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1EMG Resolution: 1.9→26.33 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 651343.49 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 1 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 47.3838 Å2 / ksol: 0.329639 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 37.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.9→26.33 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→2.02 Å / Rfactor Rfree error: 0.026 / Total num. of bins used: 6
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Xplor file |
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