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- PDB-7ddv: Crystal structure of M.tuberculosis imidazole glycerol phosphate ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7ddv | ||||||
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Title | Crystal structure of M.tuberculosis imidazole glycerol phosphate dehydratase in complex with an inhibitor | ||||||
![]() | Imidazoleglycerol-phosphate dehydratase | ||||||
![]() | LYASE/LYASE INHIBITOR / Inhibitor / LYASE / 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 | ![]() ![]() | ||||||
![]() | Tiwari, S. / Pal, R.K. / Biswal, B.K. | ||||||
![]() | ![]() Title: Crystal structure of M.tuberculosis imidazole glycerol phosphate dehydratase in complex with an inhibitor Authors: Tiwari, S. / Pal, R.K. / 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 | ![]() | 59.1 KB | Display | ![]() |
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PDB format | ![]() | 38.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 784.2 KB | Display | ![]() |
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Full document | ![]() | 785.3 KB | Display | |
Data in XML | ![]() | 10.7 KB | Display | |
Data in CIF | ![]() | 14.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7dnqC ![]() 7fcyC ![]() 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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1 | ![]()
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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: 23633.516 Da / Num. of mol.: 1 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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-Non-polymers , 5 types, 131 molecules ![](data/chem/img/MN.gif)
![](data/chem/img/H3L.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/H3L.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | ChemComp-H3L / ( | #4: Chemical | ChemComp-GOL / | #5: Chemical | #6: 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: 2.47 Å3/Da / Density % sol: 50.11 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion / pH: 9 Details: 20% PEG1500, 0.2M sodium citrate tribasic dehydrate, 0.1M Tris HCL, pH 9.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Sep 29, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54178 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→35 Å / Num. obs: 12742 / % possible obs: 100 % / Redundancy: 21.5 % / CC1/2: 0.92 / Net I/σ(I): 13.56 |
Reflection shell | Resolution: 2.2→2.28 Å / Num. unique obs: 1230 / CC1/2: 0.718 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4GQU Resolution: 2.2→33.74 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.934 / SU B: 5.034 / SU ML: 0.122 / Cross valid method: FREE R-VALUE / ESU R: 0.186 / ESU R Free: 0.167 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: 24.539 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→33.74 Å
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Refine LS restraints |
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LS refinement shell |
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