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Open data
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Basic information
Entry | Database: PDB / ID: 2oky | ||||||
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Title | A non-invasive GFP-based biosensor for mercury ions | ||||||
![]() | Green fluorescent protein | ||||||
![]() | LUMINESCENT PROTEIN / mercury sensor / GFP | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Sagermann, M. / Chapleau, R.R. | ||||||
![]() | ![]() 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: ![]() Title: Local complexity of amino acid interactions in a protein core. Authors: Jain, R.K. / Ranganathan, R. #2: ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 102.7 KB | Display | ![]() |
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PDB format | ![]() | 79.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 446.9 KB | Display | ![]() |
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Full document | ![]() | 463.3 KB | Display | |
Data in XML | ![]() | 22 KB | Display | |
Data in CIF | ![]() | 29.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2okwC ![]() 1embS 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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2 | ![]()
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Unit cell |
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Details | IN the crystal, eGFP is a dimer of chains A, B. |
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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.) ![]() ![]() ![]() ![]() #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: ![]() |
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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: ![]() ![]() ![]() |
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 |
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Processing
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Refinement | Method to determine structure: ![]() 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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