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- PDB-3svd: Engineered medium-affinity halide-binding protein derived from YF... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3svd | |||||||||
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Title | Engineered medium-affinity halide-binding protein derived from YFP: bromide complex | |||||||||
![]() | Green fluorescent protein | |||||||||
![]() | HALIDE BINDING PROTEIN / beta barrel / luminescent protein / yellow fluorescent protein / imaging reagent | |||||||||
Function / homology | ![]() | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Wang, W. / Grimley, J.S. / Beese, L.S. / Hellinga, H.W. | |||||||||
![]() | ![]() Title: Determination of engineered chloride-binding site structures in fluorescent proteins reveals principles of halide recognition Authors: Wang, W. / Grimley, J.S. / Augustine, G.J. / Beese, L.S. / Hellinga, H.W. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 105.6 KB | Display | ![]() |
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PDB format | ![]() | 80 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 441 KB | Display | ![]() |
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Full document | ![]() | 442.4 KB | Display | |
Data in XML | ![]() | 13 KB | Display | |
Data in CIF | ![]() | 18.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3sryC ![]() 3ss0C ![]() 3sshC ![]() 3sskC ![]() 3sslC ![]() 3sspC ![]() 3sstC ![]() 3ssvC ![]() 3ssyC ![]() 3svbC ![]() 3svcSC ![]() 3sveC 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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Unit cell |
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Components
#1: Protein | Mass: 29307.723 Da / Num. of mol.: 1 / Mutation: Q69T, S72A, K79R, V163A, T203Y, H231L Source method: isolated from a genetically manipulated source Details: synthetic / Source: (gene. exp.) ![]() ![]() ![]() ![]() | ||||
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#2: Chemical | ChemComp-EDO / | ||||
#3: Chemical | ChemComp-BR / #4: Water | ChemComp-HOH / | Sequence details | UNP RESIDUE SER65 UNDERWENT MUTATION TO GLY. GLY65, TYR66, AND GLY67 CIRCULARIZ | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.81 Å3/Da / Density % sol: 32.14 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: 21% PEG2000, 50 mM sodium acetate, 90 mM magnesium chloride, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 290K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 11, 2009 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9199 Å / Relative weight: 1 |
Reflection | Resolution: 1.78→40.53 Å / Num. all: 20972 / Num. obs: 20909 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 3SVC Resolution: 1.78→40.53 Å / Occupancy max: 1 / Occupancy min: 0.34 / SU ML: 0.41 / σ(F): 1.34 / Phase error: 18.29 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.77 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 44.968 Å2 / ksol: 0.41 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.78→40.53 Å
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Refine LS restraints |
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LS refinement shell |
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