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Yorodumi- PDB-3hem: Structure of Mycobacterium tuberculosis Mycolic Acid Cyclopropane... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3hem | ||||||
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Title | Structure of Mycobacterium tuberculosis Mycolic Acid Cyclopropane Synthase CmaA2 in Complex with Dioctylamine | ||||||
Components | Cyclopropane-fatty-acyl-phospholipid synthase 2 | ||||||
Keywords | TRANSFERASE / Protein-ligand complex / Cytoplasm / Lipid synthesis / Methyltransferase / S-adenosyl-L-methionine | ||||||
Function / homology | Function and homology information cyclopropane-fatty-acyl-phospholipid synthase / cyclopropane-fatty-acyl-phospholipid synthase activity / Actinobacterium-type cell wall biogenesis / symbiont-mediated perturbation of host innate immune response / mycolate cell wall layer assembly / mycolic acid biosynthetic process / S-adenosylmethionine metabolic process / lipid biosynthetic process / methylation / response to hypoxia ...cyclopropane-fatty-acyl-phospholipid synthase / cyclopropane-fatty-acyl-phospholipid synthase activity / Actinobacterium-type cell wall biogenesis / symbiont-mediated perturbation of host innate immune response / mycolate cell wall layer assembly / mycolic acid biosynthetic process / S-adenosylmethionine metabolic process / lipid biosynthetic process / methylation / response to hypoxia / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Mycobacterium tuberculosis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.39 Å | ||||||
Authors | Liu, Z. / Sacchettini, J.C. | ||||||
Citation | Journal: TO BE PUBLISHED Title: Structure of Mycobacterium tuberculosis Mycolic Acid Cyclopropane Synthase CmaA2 in Complex with Dioctylamine Authors: Barkan, D. / Liu, Z. / Sacchettini, J.C. / Glickman, M.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3hem.cif.gz | 71.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3hem.ent.gz | 53.9 KB | Display | PDB format |
PDBx/mmJSON format | 3hem.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/he/3hem ftp://data.pdbj.org/pub/pdb/validation_reports/he/3hem | HTTPS FTP |
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-Related structure data
Similar structure data |
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-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: 34642.023 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: cma2, cmaA2, MT0524, MTCY20G9.30c, Rv0503c / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) References: UniProt: P0A5P0, UniProt: P9WPB5*PLUS, cyclopropane-fatty-acyl-phospholipid synthase |
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#2: Chemical | ChemComp-D22 / |
#3: Chemical | ChemComp-CO3 / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.63 Å3/Da / Density % sol: 73.46 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 Details: pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9795 Å |
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Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.39→50 Å / Num. obs: 23172 / Biso Wilson estimate: 68.445 Å2 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.39→48.261 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7 / Stereochemistry target values: ML
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Solvent computation | Bsol: 60.738 Å2 / ksol: 0.388 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 118.09 Å2 / Biso mean: 65.993 Å2 / Biso min: 25.01 Å2
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Refinement step | Cycle: LAST / Resolution: 2.39→48.261 Å
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Refine LS restraints |
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LS refinement shell |
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