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Yorodumi- PDB-6aie: Crystal structure of a new form of RsmD-like RNA methyl transfera... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6aie | ||||||
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Title | Crystal structure of a new form of RsmD-like RNA methyl transferase from Mycobacterium tuberculosis determined at 1.74 A resolution | ||||||
Components | Putative methyltransferase | ||||||
Keywords | TRANSFERASE | ||||||
Function / homology | Function and homology information 16S rRNA (guanine(966)-N(2))-methyltransferase activity / 16S rRNA (guanine966-N2)-methyltransferase / host cell nucleolus / rRNA methylation / Transferases; Transferring one-carbon groups; Methyltransferases / methyltransferase activity / host cell cytoplasm / nucleic acid binding / extracellular region Similarity search - Function | ||||||
Biological species | Mycobacterium tuberculosis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.74 Å | ||||||
Authors | Venkataraman, S. / Dhankar, A. / Sinha, K.M. / Manivasakan, P. / Iqbal, N. / Singh, T.P. / Prasad, B.V.L.S. | ||||||
Citation | Journal: To Be Published Title: Crystal structure of a new form of RsmD-like RNA methyl transferase from Mycobacterium tuberculosis determined at 1.74 A resolution Authors: Venkataraman, S. / Dhankar, A. / Sinha, K.M. / Bandopadhyay, K. / Iqbal, N. / Singh, T.P. / Prasad, V.L.S.B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6aie.cif.gz | 118.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6aie.ent.gz | 91.2 KB | Display | PDB format |
PDBx/mmJSON format | 6aie.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6aie_validation.pdf.gz | 442.3 KB | Display | wwPDB validaton report |
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Full document | 6aie_full_validation.pdf.gz | 447.2 KB | Display | |
Data in XML | 6aie_validation.xml.gz | 24.2 KB | Display | |
Data in CIF | 6aie_validation.cif.gz | 35.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ai/6aie ftp://data.pdbj.org/pub/pdb/validation_reports/ai/6aie | 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
#1: Protein | Mass: 19914.572 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Details: SF file contains Friedel pairs. / Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) Gene: rsmD, ERS007661_01921, ERS007663_00818, ERS007665_01852, ERS007672_04225, ERS007681_00248, ERS007722_02698, ERS007739_01109, ERS007741_03599, ERS023446_00051, ERS027646_01755, ERS027651_01374, ...Gene: rsmD, ERS007661_01921, ERS007663_00818, ERS007665_01852, ERS007672_04225, ERS007681_00248, ERS007722_02698, ERS007739_01109, ERS007741_03599, ERS023446_00051, ERS027646_01755, ERS027651_01374, ERS027652_01710, ERS027654_02036, ERS027656_00358, ERS027659_03553, ERS031537_04978, SAMEA2682864_00651, SAMEA2683035_02297 Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: A0A045IDU3, UniProt: I6XFS7*PLUS, 16S rRNA (guanine966-N2)-methyltransferase #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.23 Å3/Da / Density % sol: 44.91 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / Details: 2M Potassium acetate, 100mM Tris (PH 7.4) |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9677 Å |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: May 19, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9677 Å / Relative weight: 1 |
Reflection | Resolution: 1.74→100.8 Å / Num. obs: 57366 / % possible obs: 98.7 % / Redundancy: 3 % / Rsym value: 0.153 / Net I/σ(I): 5.6 |
Reflection shell | Resolution: 1.74→1.77 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.019 / Mean I/σ(I) obs: 5.6 / Num. unique obs: 3777 / Rsym value: 0.669 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3P9N Resolution: 1.74→50.39 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.92 / SU B: 4.466 / SU ML: 0.129 / Cross valid method: THROUGHOUT / ESU R: 0.133 / ESU R Free: 0.124 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.349 Å2
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Refinement step | Cycle: 1 / Resolution: 1.74→50.39 Å
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Refine LS restraints |
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