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Yorodumi- PDB-1o9g: rRNA methyltransferase aviRa from Streptomyces viridochromogenes ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1o9g | ||||||
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Title | rRNA methyltransferase aviRa from Streptomyces viridochromogenes at 1.5A | ||||||
Components | RRNA METHYLTRANSFERASE | ||||||
Keywords | TRANSFERASE / ANTIBIOTIC RESISTANCE / RRNA-METHYLTRANSFERASE / SE-MAD | ||||||
Function / homology | Function and homology information 23S rRNA (guanine2535-N1)-methyltransferase / rRNA (guanine-N1-)-methyltransferase activity / rRNA methylation / methylation / response to antibiotic Similarity search - Function | ||||||
Biological species | STREPTOMYCES VIRIDOCHROMOGENES (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.5 Å | ||||||
Authors | Mosbacher, T.G. / Schulz, G.E. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2003 Title: Crystal Structure of the Avilamycin Resistance-Conferring Methyltransferase Avira from Streptomyces Viridochromogenes Authors: Mosbacher, T.G. / Bechthold, A. / Schulz, G.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1o9g.cif.gz | 113.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1o9g.ent.gz | 92.5 KB | Display | PDB format |
PDBx/mmJSON format | 1o9g.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1o9g_validation.pdf.gz | 424.9 KB | Display | wwPDB validaton report |
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Full document | 1o9g_full_validation.pdf.gz | 428.4 KB | Display | |
Data in XML | 1o9g_validation.xml.gz | 14.9 KB | Display | |
Data in CIF | 1o9g_validation.cif.gz | 22.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o9/1o9g ftp://data.pdbj.org/pub/pdb/validation_reports/o9/1o9g | HTTPS FTP |
-Related 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: 26833.492 Da / Num. of mol.: 1 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) STREPTOMYCES VIRIDOCHROMOGENES (bacteria) Plasmid: PRSETB / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): B834 / Variant (production host): SE-MET / References: UniProt: Q9F5K5 |
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#2: Water | ChemComp-HOH / |
Compound details | ENGINEERED MUTATION ILE 11 MET, ARG 190 GLY AND LEU 239 MET. ALSO SEE REMARK 999 FOR MORE DETAILS ...ENGINEERED |
Sequence details | SEQUENCE IN DATABASE INCORRECT FROM RESIDUE 180 TO 195. THE SWISS-PROT ACCESSION Q9F5K5 HAS THE ...SEQUENCE IN DATABASE INCORRECT FROM RESIDUE 180 TO 195. THE SWISS-PROT ACCESSION Q9F5K5 HAS THE SEQUENCE SARTGKGRCP |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2 Å3/Da / Density % sol: 39 % | ||||||||||||||||||||||||
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Crystal grow | pH: 6.9 / Details: PEG 20000 9%, MES 6.6, pH 6.90 | ||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / Method: vapor diffusion, hanging drop / PH range low: 6.9 / PH range high: 6.6 | ||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7A / Wavelength: 0.9774 |
Detector | Date: Sep 8, 2002 |
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9774 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→37.8 Å / Num. obs: 64711 / % possible obs: 97 % / Observed criterion σ(I): 2 / Redundancy: 4.3 % / Rsym value: 0.034 / Net I/σ(I): 38.7 |
Reflection shell | Resolution: 1.5→1.52 Å / Redundancy: 3.4 % / Mean I/σ(I) obs: 6.6 / Rsym value: 0.2 / % possible all: 90 |
Reflection | *PLUS Highest resolution: 1.5 Å / Lowest resolution: 15 Å / % possible obs: 97 % / Redundancy: 4.3 % / Num. measured all: 289006 / Rmerge(I) obs: 0.039 |
Reflection shell | *PLUS % possible obs: 90 % / Redundancy: 3.4 % / Num. unique obs: 1482 / Rmerge(I) obs: 0.2 / Mean I/σ(I) obs: 6.6 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.5→37.8 Å / SU B: 1.232 / SU ML: 0.047 / Cross valid method: THROUGHOUT / ESU R Free: 0.082 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Displacement parameters | Biso mean: 9.096 Å2
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Refinement step | Cycle: LAST / Resolution: 1.5→37.8 Å
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Refinement | *PLUS Highest resolution: 1.5 Å / Lowest resolution: 25 Å / Num. reflection obs: 33212 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS
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