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- PDB-7pci: BurG (holo) in complex with hydroxypyruvate-enol (8): Biosynthesi... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7pci | ||||||
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Title | BurG (holo) in complex with hydroxypyruvate-enol (8): Biosynthesis of cyclopropanol rings in bacterial toxins | ||||||
![]() | Ketol-acid reductoisomerase | ||||||
![]() | LYASE / Pathogens / Natural Products / Toxins / Biosynthesis / Catalysis | ||||||
Function / homology | ![]() ketol-acid reductoisomerase (NADP+) / ketol-acid reductoisomerase activity / valine biosynthetic process / isoleucine biosynthetic process / amino acid biosynthetic process / nucleotide binding / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Trottmann, F. / Ishida, K. / Ishida, M. / Kries, H. / Groll, M. / Hertweck, C. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Pathogenic bacteria remodel central metabolic enzyme to build a cyclopropanol warhead. Authors: Trottmann, F. / Ishida, K. / Ishida-Ito, M. / Kries, H. / Groll, M. / Hertweck, C. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 150.6 KB | Display | ![]() |
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PDB format | ![]() | 116.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 7pccSC ![]() 7pceC ![]() 7pcgC ![]() 7pclC ![]() 7pcmC ![]() 7pcnC ![]() 7pcoC ![]() 7pctC 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, 1 molecules A
#1: Protein | Mass: 38716.699 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: ATCC 700388 / DSM 13276 / CIP 106301 / E264 / Gene: ilvC-2, BTH_II2094 / Production host: ![]() ![]() References: UniProt: Q2T3G7, ketol-acid reductoisomerase (NADP+) |
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-Non-polymers , 5 types, 69 molecules ![](data/chem/img/NAD.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/74I.gif)
![](data/chem/img/IMD.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/74I.gif)
![](data/chem/img/IMD.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-NAD / | ||||||
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#3: Chemical | #4: Chemical | ChemComp-74I / ( | #5: Chemical | ChemComp-IMD / | #6: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.9 Å3/Da / Density % sol: 35.27 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 0.1 M Imidazole; 20% PEG 6K, 2 mM NAD+, 5 mM MgCl2, 2 mM (8) |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 20, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→30 Å / Num. obs: 23699 / % possible obs: 98.4 % / Redundancy: 4.4 % / Rmerge(I) obs: 0.074 / Net I/σ(I): 11.9 |
Reflection shell | Resolution: 1.9→2 Å / Rmerge(I) obs: 0.569 / Mean I/σ(I) obs: 2.7 / Num. unique obs: 3335 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 7PCC Resolution: 1.9→30 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.953 / SU B: 12 / SU ML: 0.141 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.153 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
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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: 70.89 Å2 / Biso mean: 28.13 Å2 / Biso min: 19.72 Å2
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Refinement step | Cycle: final / Resolution: 1.9→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.949 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 3.052 Å / Origin y: -27.552 Å / Origin z: 13.059 Å
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Refinement TLS group |
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