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- PDB-7q2f: mycolic acid methyltransferase Hma (MmaA4) from Mycobac-terium tu... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7q2f | |||||||||
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Title | mycolic acid methyltransferase Hma (MmaA4) from Mycobac-terium tuberculosis in complex with ZT585 | |||||||||
![]() | Hydroxymycolate synthase MmaA4 | |||||||||
![]() | TRANSFERASE / mycolic acid methyltransferase mycobacterium tuberculosis fragment based ligand discovery | |||||||||
Function / homology | ![]() mycolic acid biosynthetic process / S-adenosylmethionine-dependent methyltransferase activity / peptidoglycan-based cell wall / Transferases; Transferring one-carbon groups; Methyltransferases / methyltransferase activity / methylation / plasma membrane Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Maveyraud, L. / Galy, R. / Mourey, L. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Fragment-Based Ligand Discovery Applied to the Mycolic Acid Methyltransferase Hma (MmaA4) from Mycobacterium tuberculosis : A Crystallographic and Molecular Modelling Study. Authors: Galy, R. / Ballereau, S. / Genisson, Y. / Mourey, L. / Plaquevent, J.C. / Maveyraud, L. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 134.5 KB | Display | ![]() |
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PDB format | ![]() | 102.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 455.7 KB | Display | ![]() |
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Full document | ![]() | 458.5 KB | Display | |
Data in XML | ![]() | 13.9 KB | Display | |
Data in CIF | ![]() | 20 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7q2bC ![]() 7q2cC ![]() 7q2dC ![]() 7q2eC ![]() 7q2gC ![]() 7q2hC ![]() 2fk7S C: citing same article ( S: Starting model for refinement |
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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
#1: Protein | Mass: 36521.305 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: ATCC 25618 / H37Rv / Gene: mmaA4, hma, mma4, Rv0642c / Plasmid: pET15b / Production host: ![]() ![]() References: UniProt: Q79FX8, Transferases; Transferring one-carbon groups; Methyltransferases | ||||||
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#2: Chemical | ChemComp-EDO / | ||||||
#3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.64 Å3/Da / Density % sol: 53.33 % |
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Crystal grow | Temperature: 285 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: BisTris 50 mM, PEG 3350 4% (w/v), pH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 23, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.95373 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→49.46 Å / Num. obs: 33526 / % possible obs: 98.3 % / Redundancy: 5.9 % / CC1/2: 0.98 / Rrim(I) all: 0.175 / Net I/σ(I): 7.2 |
Reflection shell | Resolution: 1.85→1.88 Å / Redundancy: 5.2 % / Mean I/σ(I) obs: 1.4 / Num. unique obs: 1649 / CC1/2: 0.531 / Rrim(I) all: 1.299 / % possible all: 99.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2FK7 Resolution: 1.85→49.46 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.944 / SU B: 6.346 / SU ML: 0.095 / Cross valid method: THROUGHOUT / ESU R: 0.121 / ESU R Free: 0.121 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE 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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 50.812 Å2
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Refinement step | Cycle: 1 / Resolution: 1.85→49.46 Å
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Refine LS restraints |
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