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- PDB-4xdz: Holo structure of ketol-acid reductoisomerase from Ignisphaera ag... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4xdz | ||||||
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Title | Holo structure of ketol-acid reductoisomerase from Ignisphaera aggregans | ||||||
![]() | Ketol-acid reductoisomerase | ||||||
![]() | OXIDOREDUCTASE / Rossmann fold | ||||||
Function / homology | ![]() ketol-acid reductoisomerase [NAD(P)+] / ketol-acid reductoisomerase activity / valine biosynthetic process / isoleucine biosynthetic process / amino acid biosynthetic process / NADP binding / magnesium ion binding / cytosol 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 | ![]() | 304.8 KB | Display | ![]() |
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PDB format | ![]() | 246 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 | ![]() | 33.6 KB | Display | |
Data in CIF | ![]() | 49.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4xdyC ![]() 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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Details | biological unit is the same as asym. |
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Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 38465.508 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: E0SRA9, ketol-acid reductoisomerase (NADP+) |
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-Non-polymers , 6 types, 610 molecules ![](data/chem/img/NDP.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/40E.gif)
![](data/chem/img/EPE.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/40E.gif)
![](data/chem/img/EPE.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | ChemComp-MG / #4: Chemical | #5: Chemical | #6: Chemical | ChemComp-GOL / #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.31 Å3/Da / Density % sol: 46.7 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6 Details: 0.1 M bis-tris pH 6, 22% polyethylene glycol monomethylether 5000 |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 24, 2014 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 1.15→68.415 Å / Num. obs: 236179 / % possible obs: 95 % / Redundancy: 3 % / Rpim(I) all: 0.054 / Rrim(I) all: 0.096 / Rsym value: 0.079 / Net I/av σ(I): 5.195 / Net I/σ(I): 6.9 / Num. measured all: 662948 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4KQX Resolution: 1.15→68.415 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.971 / WRfactor Rfree: 0.1737 / WRfactor Rwork: 0.1413 / FOM work R set: 0.7951 / SU B: 1.683 / SU ML: 0.033 / SU R Cruickshank DPI: 0.0363 / SU Rfree: 0.0379 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.036 / ESU R Free: 0.038 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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 max: 88.77 Å2 / Biso mean: 13.086 Å2 / Biso min: 5.42 Å2
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Refinement step | Cycle: final / Resolution: 1.15→68.415 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.15→1.178 Å / Total num. of bins used: 20
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