+Open data
-Basic information
Entry | Database: PDB / ID: 2oky | ||||||
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Title | A non-invasive GFP-based biosensor for mercury ions | ||||||
Components | Green fluorescent protein | ||||||
Keywords | LUMINESCENT PROTEIN / mercury sensor / GFP | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Aequorea victoria (jellyfish) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Sagermann, M. / Chapleau, R.R. | ||||||
Citation | Journal: Protein Sci. / Year: 2008 Title: Design of a highly specific and noninvasive biosensor suitable for real-time in vivo imaging of mercury (II) uptake. Authors: Chapleau, R.R. / Blomberg, R. / Ford, P.C. / Sagermann, M. #1: Journal: Proc.Natl.Acad.Sci.USA / Year: 2004 Title: Local complexity of amino acid interactions in a protein core. Authors: Jain, R.K. / Ranganathan, R. #2: Journal: Science / Year: 1996 Title: Crystal structure of the Aequorea victoria green fluorescent protein. Authors: Ormo, M. / Cubitt, A.B. / Kallio, K. / Gross, L.A. / Tsien, R.Y. / Remington, S.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2oky.cif.gz | 102.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2oky.ent.gz | 79.5 KB | Display | PDB format |
PDBx/mmJSON format | 2oky.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ok/2oky ftp://data.pdbj.org/pub/pdb/validation_reports/ok/2oky | HTTPS FTP |
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-Related structure data
Related structure data | 2okwC 1embS 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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2 |
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Unit cell |
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Details | IN the crystal, eGFP is a dimer of chains A, B. |
-Components
#1: Protein | Mass: 26898.365 Da / Num. of mol.: 2 / Mutation: S65T, R80Q, S205C Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aequorea victoria (jellyfish) / Gene: GFP / Plasmid: pet151 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P42212 #2: Water | ChemComp-HOH / | Sequence details | AUTHORS STATE THAT RESIDUE 64 IS A LEUCINE. RESIDUE 65 HAS BEEN MUTATED FROM SER TO THR AND RESIDUE ...AUTHORS STATE THAT RESIDUE 64 IS A LEUCINE. RESIDUE 65 HAS BEEN MUTATED FROM SER TO THR AND RESIDUE 80 IS AN ARG TO GLN MUTATION. RESIDUE 80 IS LISTED AS A GLN IN THE DATABASE REFERENCE BUT IS AN ARG ACCORDING TO ROUWENDAL ET AL., 1997 PLANT MOL. BIOL. 33, 989-999 RESIDUES THR 65, TYR 66, GLY 67 CONSTITUTE | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.11 Å3/Da / Density % sol: 41.61 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 32% PEG 8000, 100mM PIPES, 200mM ammonium sulfate, pH 6.5, VAPOR DIFFUSION, HANGING DROP |
-Data collection
Diffraction | Mean temperature: 150 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.979454 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 6, 2006 / Details: Single SI crystal flat mirror |
Radiation | Monochromator: SI crystal (111) flat mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979454 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→19.936 Å / Num. all: 18687 / Num. obs: 18556 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 14.4 % / Rmerge(I) obs: 0.036 / Rsym value: 0.055 / Net I/σ(I): 38.46 |
Reflection shell | Resolution: 2.4→2.6 Å / Redundancy: 14.5 % / Rmerge(I) obs: 0.149 / Mean I/σ(I) obs: 9.99 / Num. unique all: 3838 / Rsym value: 0.33 / % possible all: 98.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1EMB Resolution: 2.4→19.9 Å / Isotropic thermal model: Anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber Details: First 6 residues and the last c-terminal residues could not be modeled into the density.
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Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.4→19.9 Å
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Refine LS restraints |
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