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- PDB-5zqn: Crystal structure of Mycobacterium tuberculosis HisB in complex w... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5zqn | |||||||||
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Title | Crystal structure of Mycobacterium tuberculosis HisB in complex with a ligand | |||||||||
![]() | Imidazoleglycerol-phosphate dehydratase | |||||||||
![]() | LYASE / HisB / Imidazoleglycerol-phosphate dehydratase / modified cysteine | |||||||||
Function / homology | ![]() imidazoleglycerol-phosphate dehydratase / imidazoleglycerol-phosphate dehydratase activity / L-histidine biosynthetic process / metal ion binding / cytoplasm Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() | |||||||||
![]() | Kumar, D. / Pal, R.K. / Biswal, B.K. | |||||||||
![]() | ![]() Title: Characterization of a triazole scaffold compound as an inhibitor of Mycobacterium tuberculosis imidazoleglycerol-phosphate dehydratase. Authors: Kumar, D. / Jha, B. / Bhatia, I. / Ashraf, A. / Dwivedy, A. / Biswal, B.K. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 94.6 KB | Display | ![]() |
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PDB format | ![]() | 72.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 450.7 KB | Display | ![]() |
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Full document | ![]() | 452.6 KB | Display | |
Data in XML | ![]() | 11.9 KB | Display | |
Data in CIF | ![]() | 16.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5xdsC ![]() 6khhC ![]() 4lomS 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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1 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 23840.830 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: H37Rv / Gene: hisB, Rv1601, MTCY336.03c / Production host: ![]() References: UniProt: P9WML9, imidazoleglycerol-phosphate dehydratase | ||||||
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#2: Chemical | #3: Chemical | ChemComp-CL / | #4: Chemical | ChemComp-IYP / ( | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.51 Å3/Da / Density % sol: 51.01 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: PEG 1500, sodium citrate tribasic dehydrate, tris HCl |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Apr 25, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54178 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→35 Å / Num. obs: 23350 / % possible obs: 99.9 % / Redundancy: 13.7 % / Rmerge(I) obs: 0.101 / Net I/σ(I): 21.08 |
Reflection shell | Resolution: 1.8→1.86 Å / Redundancy: 10.5 % / Mean I/σ(I) obs: 2.39 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4LOM Resolution: 1.8→28.2 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.962 / SU B: 2.642 / SU ML: 0.076 / Cross valid method: THROUGHOUT / ESU R: 0.097 / ESU R Free: 0.097 Details: HYDROGENS HAVE BEEN ADDED IN THEIR 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 BULK SOLVENT | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.79 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→28.2 Å
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Refine LS restraints |
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