[English] 日本語
Yorodumi- PDB-2fl1: Crystal structure of red fluorescent protein from Zoanthus, zRFP5... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2fl1 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal structure of red fluorescent protein from Zoanthus, zRFP574, at 2.4A resolution | |||||||||
Components | Red fluorescent protein zoanRFP | |||||||||
Keywords | FLUORESCENT PROTEIN / Red fluorescent protein / button polyp / Zoanthus sp. / chromophore / beta-can fold / beta barrel / tightly packed tetramer / intersubunit interface / fluorescent marker / emission maximum 574nm / zRFP574 | |||||||||
Function / homology | Green Fluorescent Protein / Green fluorescent protein / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / bioluminescence / Beta Barrel / Mainly Beta / Red fluorescent protein zoanRFP Function and homology information | |||||||||
Biological species | Zoanthus sp. (invertebrata) | |||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | |||||||||
Authors | Pletnev, V. / Pletneva, N. / Martynov, V. / Tikhonova, T. / Popov, B. / Pletnev, S. | |||||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2006 Title: Structure of a red fluorescent protein from Zoanthus, zRFP574, reveals a novel chromophore Authors: Pletneva, N. / Pletnev, S. / Tikhonova, T. / Popov, V. / Martynov, V. / Pletnev, V. | |||||||||
History |
| |||||||||
Remark 999 | SEQUENCE Chromophore (XYG 66) is formed autocatalytically from Asp-Tyr-Gly (according to nucleotide ...SEQUENCE Chromophore (XYG 66) is formed autocatalytically from Asp-Tyr-Gly (according to nucleotide sequence) after decarboxylation of Asp and other deprotonation processes. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2fl1.cif.gz | 197.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2fl1.ent.gz | 157.9 KB | Display | PDB format |
PDBx/mmJSON format | 2fl1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fl/2fl1 ftp://data.pdbj.org/pub/pdb/validation_reports/fl/2fl1 | HTTPS FTP |
---|
-Related structure data
Related structure data | 1xa9S S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
| ||||||||
Details | Two dimers in assymetric unit. The tightly packed tetramers generated by crystallographic symmetry operations (-x-1, y, -z-1/2) and (-z, y, -z-1/2) . |
-Components
#1: Protein | Mass: 25976.486 Da / Num. of mol.: 4 / Mutation: K5A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Zoanthus sp. (invertebrata) / Plasmid: pQE-30 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109DE3 / References: UniProt: Q8T4U4 #2: Chemical | ChemComp-SO4 / #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.46 Å3/Da / Density % sol: 50.01 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.9 Details: 1.5M ammonium sulphate, 0.2M K/Na Tartrate, 0.1M Na Citrate, pH 5.9, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Nov 25, 2005 |
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: 2.4→30 Å / Num. all: 40898 / Num. obs: 40878 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Redundancy: 5.2 % / Rmerge(I) obs: 0.135 / Net I/σ(I): 11.1 |
Reflection shell | Resolution: 2.4→2.49 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.66 / Mean I/σ(I) obs: 2.1 / Num. unique all: 4051 / % possible all: 99.9 |
-Processing
Software |
| |||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1XA9 Resolution: 2.4→30 Å / Isotropic thermal model: Isotropic / Cross valid method: Rfree throughout / σ(F): 0 / Stereochemistry target values: Engh & Huber Details: Cross validated maximum likelihood, simulated annealing refinement
| |||||||||||||||||||||
Displacement parameters | Biso mean: 28.8 Å2 | |||||||||||||||||||||
Refine analyze |
| |||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→30 Å
| |||||||||||||||||||||
Refine LS restraints |
|