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- PDB-8qnf: Crystal structure of the Condensation domain TomBC from the Tomay... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8qnf | ||||||
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Title | Crystal structure of the Condensation domain TomBC from the Tomaymycin non-ribosomal peptide synthetase | ||||||
![]() | Condensation domain TomBC from the Tomaymycin non-ribosomal peptide synthetase | ||||||
![]() | BIOSYNTHETIC PROTEIN / Non-ribosomal peptide synthetase / Tomaymycin / Condensation | ||||||
Function / homology | FORMIC ACID / : ![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Karanth, M. / Schmelz, S. / Kirkpatrick, J. / Krausze, J. / Scrima, A. / Carlomagno, T. | ||||||
Funding support | ![]()
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![]() | ![]() Title: The specificity of intermodular recognition in a prototypical nonribosomal peptide synthetase depends on an adaptor domain. Authors: Karanth, M.N. / Kirkpatrick, J.P. / Krausze, J. / Schmelz, S. / Scrima, A. / Carlomagno, T. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 244.7 KB | Display | ![]() |
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PDB format | ![]() | 160.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 464.2 KB | Display | ![]() |
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Full document | ![]() | 471.9 KB | Display | |
Data in XML | ![]() | 23.3 KB | Display | |
Data in CIF | ![]() | 35.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8qpyC ![]() 8qrxC ![]() 8qsxC ![]() 8rz6C 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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Unit cell |
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Components on special symmetry positions |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 59291.016 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: TomBC / Source: (gene. exp.) ![]() ![]() ![]() |
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-Non-polymers , 5 types, 382 molecules ![](data/chem/img/FMT.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/K.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/K.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-FMT / #3: Chemical | #4: Chemical | ChemComp-NA / #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.3 Å3/Da / Density % sol: 63 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop Details: Protein (stored in 50mM Kpi, 150 mM NaCl, pH 7.0) crystallised at 30mg/mL at 4 degC in 100 mM Tris pH 8.5, 3.5 M NaFormate 25% glycerol used as cryoprotectant. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 7, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97625 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→19.94 Å / Num. obs: 81329 / % possible obs: 85 % / Redundancy: 4.9 % / Biso Wilson estimate: 30.63 Å2 / CC1/2: 0.997 / Net I/σ(I): 12.43 |
Reflection shell | Resolution: 1.65→1.7 Å / Mean I/σ(I) obs: 2.01 / Num. unique obs: 2759 / CC1/2: 0.694 |
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Processing
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Refinement | Method to determine structure: ![]() Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 38.34 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.65→19.94 Å
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Refine LS restraints |
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LS refinement shell |
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