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- PDB-7svt: Mycobacterium tuberculosis 3-hydroxyl-ACP dehydratase HadAB in co... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7svt | ||||||
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Title | Mycobacterium tuberculosis 3-hydroxyl-ACP dehydratase HadAB in complex with 1,3-diarylpyrazolyl-acylsulfonamide inhibitor | ||||||
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![]() | LYASE/INHIBITOR / ![]() ![]() | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Krieger, I.V. / Sacchettini, J.C. / TB Structural Genomics Consortium (TBSGC) | ||||||
Funding support | ![]()
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![]() | ![]() Title: 1,3-Diarylpyrazolyl-acylsulfonamides Target HadAB/BC Complex in Mycobacterium tuberculosis . Authors: Singh, V. / Grzegorzewicz, A.E. / Fienberg, S. / Muller, R. / Khonde, L.P. / Sanz, O. / Alfonso, S. / Urones, B. / Drewes, G. / Bantscheff, M. / Ghidelli-Disse, S. / Ioerger, T.R. / Angala, ...Authors: Singh, V. / Grzegorzewicz, A.E. / Fienberg, S. / Muller, R. / Khonde, L.P. / Sanz, O. / Alfonso, S. / Urones, B. / Drewes, G. / Bantscheff, M. / Ghidelli-Disse, S. / Ioerger, T.R. / Angala, B. / Liu, J. / Lee, R.E. / Sacchettini, J.C. / Krieger, I.V. / Jackson, M. / Chibale, K. / Ghorpade, S.R. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 236 KB | Display | ![]() |
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PDB format | ![]() | 190.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4rlwS S: Starting model for refinement |
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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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2 | ![]()
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4 | ![]()
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Unit cell |
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Components
-Protein , 2 types, 8 molecules AHOVBIPW
#1: Protein | Mass: 17497.449 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() #2: Protein | ( Mass: 14949.993 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() References: UniProt: A0A045H5L3, ![]() |
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-Non-polymers , 5 types, 97 molecules ![](data/chem/img/CI7.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-CI7 / #4: Chemical | ![]() #5: Chemical | ![]() #6: Chemical | ChemComp-GOL / | ![]() #7: 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: 2.5 Å3/Da / Density % sol: 50.84 % |
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Crystal grow![]() | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 3.5 / Details: 0.1 M citric acid, pH 3.5, 25% PEG3350 |
-Data collection
Diffraction | Mean temperature: 120 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jul 11, 2021 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength![]() | ||||||||||||||||||||||||||||||
Reflection | Resolution: 2.4→48.64 Å / Num. obs: 51577 / % possible obs: 99.9 % / Redundancy: 5.8 % / CC1/2: 0.994 / Rmerge(I) obs: 0.198 / Rpim(I) all: 0.088 / Rrim(I) all: 0.217 / Net I/σ(I): 7.5 / Num. measured all: 299707 / Scaling rejects: 208 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: PDB entry 4rlw Resolution: 2.4→45.38 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 33.29 / 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: 159.8 Å2 / Biso mean: 53.7115 Å2 / Biso min: 22.18 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.4→45.38 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 18
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