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Yorodumi- PDB-6m1c: Crystal structure of RsmD methyltransferase of M. tuberculosis in... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6m1c | ||||||
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Title | Crystal structure of RsmD methyltransferase of M. tuberculosis in complex with sinefungin reveals key interactions | ||||||
Components | Possible methyltransferase (Methylase) | ||||||
Keywords | TRANSFERASE / Rossmann fold / RsmD / Rv2966c / M. tuberculosis | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Mycobacterium tuberculosis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.401 Å | ||||||
Authors | Bijpuria, S. / Khan, S.H. / Kumar, A. / Taneja, B. | ||||||
Funding support | India, 1items
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Citation | Journal: To Be Published Title: Crystal structure of RsmD methyltransferase of M. tuberculosis in complex with sinefungin reveals key interactions Authors: Bijpuria, S. / Khan, S.H. / Kumar, A. / Taneja, B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6m1c.cif.gz | 51.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6m1c.ent.gz | 34.2 KB | Display | PDB format |
PDBx/mmJSON format | 6m1c.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6m1c_validation.pdf.gz | 687.9 KB | Display | wwPDB validaton report |
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Full document | 6m1c_full_validation.pdf.gz | 689.9 KB | Display | |
Data in XML | 6m1c_validation.xml.gz | 9.9 KB | Display | |
Data in CIF | 6m1c_validation.cif.gz | 12.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m1/6m1c ftp://data.pdbj.org/pub/pdb/validation_reports/m1/6m1c | HTTPS FTP |
-Related structure data
Related structure data | 3p9nS 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: 19914.572 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: Rv2966c / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: I6XFS7 |
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#2: Chemical | ChemComp-SFG / |
#3: Chemical | ChemComp-ACT / |
#4: 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: 2.21 Å3/Da / Density % sol: 44.47 % |
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Crystal grow | Temperature: 297 K / Method: vapor diffusion, hanging drop / pH: 7.4 / Details: 0.1 MTris-HCl, 3.2 M Potassium acetate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.887821 Å |
Detector | Type: DECTRIS EIGER2 X 4M / Detector: PIXEL / Date: Feb 10, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.887821 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→47.8 Å / Num. obs: 7293 / % possible obs: 100 % / Redundancy: 9.2 % / CC1/2: 0.999 / Net I/σ(I): 12 |
Reflection shell | Resolution: 2.4→2.49 Å / Num. unique obs: 745 / CC1/2: 0.939 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3P9N Resolution: 2.401→47.8 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 29.73
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.401→47.8 Å
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Refine LS restraints |
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LS refinement shell |
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