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- PDB-8epz: Crystal structure of Fe-S cluster-dependent dehydratase from Para... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8epz | ||||||
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Title | Crystal structure of Fe-S cluster-dependent dehydratase from Paralcaligenes ureilyticus in complex with Mn | ||||||
![]() | Dihydroxyacid dehydratase | ||||||
![]() | LYASE / Fe-S dehydratase / sugar-acid dehydratase / ilvD/EDD family / DHAD | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Bayaraa, T. / Lonhienne, T. / Guddat, L.W. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Crystal structure of Fe-S cluster-dependent dehydratase from Paralcaligenes ureilyticus in complex with Mg Authors: Bayaraa, T. / Lonhienne, T. / Guddat, L.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 | ![]() | 224.4 KB | Display | ![]() |
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PDB format | ![]() | 177.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.4 MB | Display | ![]() |
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Full document | ![]() | 2.5 MB | Display | |
Data in XML | ![]() | 43 KB | Display | |
Data in CIF | ![]() | 58 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8ej0SC S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 62651.746 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Non-polymers , 5 types, 78 molecules ![](data/chem/img/FES.gif)
![](data/chem/img/MN.gif)
![](data/chem/img/CO2.gif)
![](data/chem/img/BCT.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MN.gif)
![](data/chem/img/CO2.gif)
![](data/chem/img/BCT.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | ChemComp-BCT / | #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.99 Å3/Da / Density % sol: 38.34 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.2 M succinic acid, 15% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Apr 21, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.954 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→48.107 Å / Num. obs: 44640 / % possible obs: 98.8 % / Redundancy: 5.3 % / Rmerge(I) obs: 0.108 / Rpim(I) all: 0.046 / Net I/σ(I): 9.1 |
Reflection shell | Resolution: 2.6→2.987 Å / Rmerge(I) obs: 0.747 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 3904 / Rpim(I) all: 0.316 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 8EJ0 Resolution: 2.6→48.107 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 32.35 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 107.05 Å2 / Biso mean: 61.2977 Å2 / Biso min: 30 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.6→48.107 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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