+Open data
-Basic information
Entry | Database: PDB / ID: 6khh | |||||||||
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Title | Crystal Structure of HisB from Mycobacterium tuberculosis | |||||||||
Components | Imidazoleglycerol-phosphate dehydratase | |||||||||
Keywords | LYASE / dehydratase | |||||||||
Function / homology | Function and homology information imidazoleglycerol-phosphate dehydratase / imidazoleglycerol-phosphate dehydratase activity / L-histidine biosynthetic process / metal ion binding / cytoplasm Similarity search - Function | |||||||||
Biological species | Mycobacterium tuberculosis (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.65 Å | |||||||||
Authors | Kumar, D. / Jha, B. / Pal, R.K. / Biswal, B.K. | |||||||||
Citation | Journal: Proteins / Year: 2021 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6khh.cif.gz | 60.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6khh.ent.gz | 40.8 KB | Display | PDB format |
PDBx/mmJSON format | 6khh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kh/6khh ftp://data.pdbj.org/pub/pdb/validation_reports/kh/6khh | HTTPS FTP |
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-Related structure data
Related structure data | 5xdsC 5zqnC 4gquS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-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: 20985.520 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) Gene: hisB, ERS007670_03574, ERS007672_02943, ERS007679_00418, ERS007681_01092, ERS023446_00531, ERS024213_01935, ERS027646_00106 Production host: Mycolicibacterium smegmatis (bacteria) References: UniProt: A0A0T7LD88, UniProt: P9WML9*PLUS, imidazoleglycerol-phosphate dehydratase | ||||||||
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#2: Chemical | #3: Chemical | ChemComp-CL / | #4: Chemical | ChemComp-ACM / | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.83 Å3/Da / Density % sol: 56.6 % |
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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 / Serial crystal experiment: N |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.54178 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Apr 21, 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: 1.65→35 Å / Num. obs: 29997 / % possible obs: 99.8 % / Redundancy: 31.4 % / CC1/2: 0.993 / Net I/σ(I): 27.02 |
Reflection shell | Resolution: 1.65→1.71 Å / Rmerge(I) obs: 0.782 / Mean I/σ(I) obs: 2.13 / Num. unique obs: 2910 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4GQU Resolution: 1.65→33.96 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.957 / SU B: 2.201 / SU ML: 0.068 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.087 / ESU R Free: 0.086 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 61.41 Å2 / Biso mean: 19.42 Å2 / Biso min: 10.17 Å2
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Refinement step | Cycle: final / Resolution: 1.65→33.96 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.65→1.691 Å / Rfactor Rfree error: 0
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