+Open data
-Basic information
Entry | Database: PDB / ID: 1i9g | ||||||
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Title | CRYSTAL STRUCTURE OF AN ADOMET DEPENDENT METHYLTRANSFERASE | ||||||
Components | HYPOTHETICAL PROTEIN RV2118C | ||||||
Keywords | TRANSFERASE / mycobacterium / MTase / AdoMet / crystal / Structural Genomics / PSI / Protein Structure Initiative / TB Structural Genomics Consortium / TBSGC | ||||||
Function / homology | Function and homology information tRNA (adenine58-N1)-methyltransferase / : / tRNA (m1A) methyltransferase complex / tRNA methylation / S-adenosylmethionine-dependent methyltransferase activity / plasma membrane Similarity search - Function | ||||||
Biological species | Mycobacterium tuberculosis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MIR / Resolution: 1.98 Å | ||||||
Authors | Gupta, A. / Kumar, P.H. / Dineshkumar, T.K. / Varshney, U. / Subramanya, H.S. / TB Structural Genomics Consortium (TBSGC) | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2001 Title: Crystal structure of Rv2118c: an AdoMet-dependent methyltransferase from Mycobacterium tuberculosis H37Rv. Authors: Gupta, A. / Kumar, P.H. / Dineshkumar, T.K. / Varshney, U. / Subramanya, H.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1i9g.cif.gz | 66.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1i9g.ent.gz | 49 KB | Display | PDB format |
PDBx/mmJSON format | 1i9g.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1i9g_validation.pdf.gz | 689.4 KB | Display | wwPDB validaton report |
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Full document | 1i9g_full_validation.pdf.gz | 693.6 KB | Display | |
Data in XML | 1i9g_validation.xml.gz | 14.3 KB | Display | |
Data in CIF | 1i9g_validation.cif.gz | 20.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i9/1i9g ftp://data.pdbj.org/pub/pdb/validation_reports/i9/1i9g | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 30160.506 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: RV2118C / Plasmid: PQE60 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21DE3 / References: UniProt: O33253, UniProt: P9WFZ1*PLUS |
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#2: Chemical | ChemComp-SAM / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 3.3 Å3/Da / Density % sol: 62.7 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Method: vapor diffusion, hanging drop / Details: VAPOR DIFFUSION, HANGING DROP | ||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 25 ℃ / pH: 7.5 | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.98→10 Å / Num. all: 70596 / Num. obs: 27574 / % possible obs: 98 % / Rsym value: 0.049 |
Reflection | *PLUS % possible obs: 98 % / Num. measured all: 70596 / Rmerge(I) obs: 0.049 |
-Processing
Software |
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Refinement | Method to determine structure: MIR / Resolution: 1.98→10 Å /
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Refinement step | Cycle: LAST / Resolution: 1.98→10 Å
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Refine LS restraints |
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Software | *PLUS Name: REFMAC / Classification: refinement | ||||||||||||
Refinement | *PLUS Lowest resolution: 10 Å / Rfactor obs: 0.205 | ||||||||||||
Solvent computation | *PLUS | ||||||||||||
Displacement parameters | *PLUS | ||||||||||||
Refine LS restraints | *PLUS
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