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- PDB-4xdy: Structure of NADH-preferring ketol-acid reductoisomerase from an ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4xdy | ||||||
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Title | Structure of NADH-preferring ketol-acid reductoisomerase from an uncultured archean | ||||||
![]() | Ketol-acid reductoisomerase | ||||||
![]() | OXIDOREDUCTASE / Rossmann fold | ||||||
Function / homology | ![]() ketol-acid reductoisomerase (NAD+) / ketol-acid reductoisomerase activity / valine biosynthetic process / isoleucine biosynthetic process / NADP binding / magnesium ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Cahn, J.K.B. / Brinkmann-Chen, S. / Arnold, F.H. | ||||||
![]() | ![]() Title: Cofactor specificity motifs and the induced fit mechanism in class I ketol-acid reductoisomerases. Authors: Cahn, J.K. / Brinkmann-Chen, S. / Spatzal, T. / Wiig, J.A. / Buller, A.R. / Einsle, O. / Hu, Y. / Ribbe, M.W. / Arnold, F.H. #1: ![]() Title: Uncovering rare NADH-preferring ketol-acid reductoisomerases. Authors: Brinkmann-Chen, S. / Cahn, J.K. / Arnold, F.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 | ![]() | 158.4 KB | Display | ![]() |
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PDB format | ![]() | 122.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 29.8 KB | Display | |
Data in CIF | ![]() | 42.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4xdzC ![]() 4xehC ![]() 4xiyC ![]() 4kqxS S: Starting model for refinement C: citing same article ( |
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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
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 37730.156 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: ilvC, GZ26G2_30 / Plasmid: pET22b(+) / Production host: ![]() ![]() References: UniProt: Q64BR7, ketol-acid reductoisomerase (NADP+) |
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-Non-polymers , 5 types, 371 molecules ![](data/chem/img/MG.gif)
![](data/chem/img/NAI.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HIO.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/NAI.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HIO.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-MG / #3: Chemical | #4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.51 Å3/Da / Density % sol: 64.98 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5 Details: 0.1 M bis-tris pH 5, 20% w/v polyethylene glycol 1500 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 30, 2013 |
Radiation | Monochromator: LIQUID NITROGEN-COOLED DOUBLE CRYSTAL K-B FOCUSING MIRRORS Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.535→102.57 Å / Num. obs: 157419 / % possible obs: 99.4 % / Redundancy: 4.5 % / Rsym value: 0.088 / Net I/σ(I): 7.2 |
Reflection shell | Resolution: 1.535→1.7 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.963 / Mean I/σ(I) obs: 1.5 / % possible all: 99.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4KQX Resolution: 1.535→102.57 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.959 / SU B: 1.989 / SU ML: 0.064 / Cross valid method: THROUGHOUT / ESU R: 0.061 / ESU R Free: 0.066 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.89 Å2
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Refinement step | Cycle: LAST / Resolution: 1.535→102.57 Å
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Refine LS restraints |
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