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Yorodumi- PDB-7q2h: mycolic acid methyltransferase Hma (MmaA4) from Mycobac-terium tu... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7q2h | |||||||||
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Title | mycolic acid methyltransferase Hma (MmaA4) from Mycobac-terium tuberculosis in complex with ZT275 | |||||||||
Components | Hydroxymycolate synthase MmaA4 | |||||||||
Keywords | TRANSFERASE / mycolic acid methyltransferase mycobacterium tuberculosis fragment based ligand discovery | |||||||||
Function / homology | Function and homology information 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 | Mycobacterium tuberculosis (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.75 Å | |||||||||
Authors | Maveyraud, L. / Galy, R. / Mourey, L. | |||||||||
Funding support | France, 2items
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Citation | Journal: Pharmaceuticals / Year: 2021 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7q2h.cif.gz | 136.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7q2h.ent.gz | 104.4 KB | Display | PDB format |
PDBx/mmJSON format | 7q2h.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7q2h_validation.pdf.gz | 895.8 KB | Display | wwPDB validaton report |
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Full document | 7q2h_full_validation.pdf.gz | 895.8 KB | Display | |
Data in XML | 7q2h_validation.xml.gz | 14.2 KB | Display | |
Data in CIF | 7q2h_validation.cif.gz | 20.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q2/7q2h ftp://data.pdbj.org/pub/pdb/validation_reports/q2/7q2h | HTTPS FTP |
-Related structure data
Related structure data | 7q2bC 7q2cC 7q2dC 7q2eC 7q2fC 7q2gC 2fk7S 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
#1: Protein | Mass: 36521.305 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria) Strain: ATCC 25618 / H37Rv / Gene: mmaA4, hma, mma4, Rv0642c / Plasmid: pET15b / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: Q79FX8, Transferases; Transferring one-carbon groups; Methyltransferases | ||||||
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#2: Chemical | ChemComp-IEJ / | ||||||
#3: Chemical | #4: Chemical | ChemComp-EDO / | #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: 2.63 Å3/Da / Density % sol: 53.25 % |
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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: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9537 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 16, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→49.03 Å / Num. obs: 40075 / % possible obs: 99.5 % / Redundancy: 8.89 % / CC1/2: 0.996 / Rrim(I) all: 0.095 / Rsym value: 0.089 / Net I/σ(I): 13.72 |
Reflection shell | Resolution: 1.75→1.86 Å / Redundancy: 8.79 % / Mean I/σ(I) obs: 2.61 / Num. unique obs: 6368 / CC1/2: 0.89 / Rrim(I) all: 0.804 / Rsym value: 0.089 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 2FK7 Resolution: 1.75→49.08 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.955 / SU B: 4.531 / SU ML: 0.072 / Cross valid method: THROUGHOUT / ESU R: 0.096 / ESU R Free: 0.097 / 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: 47.357 Å2
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Refinement step | Cycle: 1 / Resolution: 1.75→49.08 Å
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