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- PDB-4q5o: Crystal structure of EctD from S. alaskensis with 2-oxoglutarate ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4q5o | ||||||
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Title | Crystal structure of EctD from S. alaskensis with 2-oxoglutarate and 5-hydroxyectoine | ||||||
![]() | Ectoine hydroxylase | ||||||
![]() | OXIDOREDUCTASE / jelly-roll or cupin fold / ectoine hydroxylase | ||||||
Function / homology | ![]() ectoine hydroxylase / phytanoyl-CoA dioxygenase activity / 2-oxoglutarate-dependent dioxygenase activity / iron ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Hoeppner, A. / Widderich, N. / Bremer, E. / Smits, S.H. | ||||||
![]() | ![]() Title: Crystal structure of the ectoine hydroxylase, a snapshot of the active site. Authors: Hoppner, A. / Widderich, N. / Lenders, M. / Bremer, E. / Smits, S.H. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 124.7 KB | Display | ![]() |
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PDB format | ![]() | 96 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 480.3 KB | Display | ![]() |
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Full document | ![]() | 491.4 KB | Display | |
Data in XML | ![]() | 23.5 KB | Display | |
Data in CIF | ![]() | 31.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4mhrSC ![]() 4mhuC 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: 35226.602 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: DSM 13593 / LMG 18877 / RB2256 / Gene: Sala_2952 / Production host: ![]() ![]() #2: Chemical | #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.37 Å3/Da / Density % sol: 48.2 % |
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Crystal grow | Temperature: 273 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 100 mM MES pH 6.0, 200 mM Ca-acetate, 30% (w/v) PEG 400 , VAPOR DIFFUSION, HANGING DROP, temperature 273K |
-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Nov 17, 2013 |
Radiation | Monochromator: Ni FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 2.64→30 Å / Num. all: 20291 / Num. obs: 20236 / % possible obs: 99.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 |
Reflection shell | Resolution: 2.64→2.74 Å / % possible all: 99.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 4MHR Resolution: 2.64→30 Å / SU ML: 0.42 / σ(F): 1.34 / Phase error: 29.95 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.64→30 Å
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Refine LS restraints |
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LS refinement shell |
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