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- PDB-5xds: Crystal structure of Mycobacterium tuberculosis HisB bound with a... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5xds | ||||||
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Title | Crystal structure of Mycobacterium tuberculosis HisB bound with an inhibitor | ||||||
![]() | Imidazoleglycerol-phosphate dehydratase | ||||||
![]() | LYASE/LYASE INHIBITOR / Mycobacterium tuberculosis / Tuberculosis / Imidazoleglycerol phosphate dehydratase / Drug target / LYASE-LYASE INHIBITOR complex | ||||||
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. / Jha, B. / Ahangar, M.S. / Kumar, B.B. | ||||||
![]() | ![]() 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 | ![]() | 60.8 KB | Display | ![]() |
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PDB format | ![]() | 41.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 446.5 KB | Display | ![]() |
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Full document | ![]() | 446.8 KB | Display | |
Data in XML | ![]() | 11.8 KB | Display | |
Data in CIF | ![]() | 17.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5zqnC ![]() 6khhC ![]() 4gquS 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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Components on special symmetry positions |
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Components
#1: Protein | Mass: 23633.516 Da / Num. of mol.: 1 / Fragment: UNP residues 2-210 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: ATCC 25618 / 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-83O / ( | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.51 Å3/Da / Density % sol: 51.04 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion 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: Jul 22, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54178 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→50 Å / Num. obs: 25229 / % possible obs: 99.9 % / Redundancy: 27.9 % / Rmerge(I) obs: 0.105 / Rpim(I) all: 0.019 / Net I/σ(I): 43.48 |
Reflection shell | Resolution: 1.75→1.81 Å / Redundancy: 9.7 % / Rmerge(I) obs: 0.769 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 2468 / Χ2: 0.713 / % possible all: 99.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4GQU Resolution: 1.75→50 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.969 / SU B: 1.984 / SU ML: 0.061 / Cross valid method: THROUGHOUT / ESU R: 0.084 / ESU R Free: 0.087 / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.587 Å2
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Refinement step | Cycle: 1 / Resolution: 1.75→50 Å
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Refine LS restraints |
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