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Yorodumi- PDB-1o9h: rRNA methyltransferase aviRa from Streptomyces viridochromogenes ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1o9h | ||||||
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Title | rRNA methyltransferase aviRa from Streptomyces viridochromogenes at 2.4A | ||||||
Components | RRNA METHYLTRANSFERASE | ||||||
Keywords | TRANSFERASE / ANTIBIOTIC RESISTANCE / RRNA-METHYLTRANSFERASE | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 2.4 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 | 1o9h.cif.gz | 59.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1o9h.ent.gz | 43.3 KB | Display | PDB format |
PDBx/mmJSON format | 1o9h.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1o9h_validation.pdf.gz | 424.8 KB | Display | wwPDB validaton report |
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Full document | 1o9h_full_validation.pdf.gz | 428.5 KB | Display | |
Data in XML | 1o9h_validation.xml.gz | 11.2 KB | Display | |
Data in CIF | 1o9h_validation.cif.gz | 14.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o9/1o9h ftp://data.pdbj.org/pub/pdb/validation_reports/o9/1o9h | HTTPS FTP |
-Related structure data
Related structure data | 1o9gSC S: Starting model for refinement C: citing same article (ref.) |
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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: 26670.760 Da / Num. of mol.: 1 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): BL21(DE3) / References: UniProt: Q9F5K5 |
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#2: Water | ChemComp-HOH / |
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: 2.14 Å3/Da / Density % sol: 39 % | ||||||||||||||||||||||||
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Crystal grow | pH: 6.6 / Details: MES 6.6,PEG 20K 11%, pH 6.60 | ||||||||||||||||||||||||
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: 287 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200B / Wavelength: 1.5418 |
Detector | Type: BRUKER / Detector: AREA DETECTOR / Date: Jan 11, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→26.4 Å / Num. obs: 8039 / % possible obs: 90 % / Observed criterion σ(I): 2 / Redundancy: 2.3 % / Rmerge(I) obs: 0.071 / Net I/σ(I): 38.7 |
Reflection shell | Resolution: 2.4→2.46 Å / Redundancy: 1.5 % / Rmerge(I) obs: 0.282 / Mean I/σ(I) obs: 3.2 / % possible all: 90 |
Reflection | *PLUS Highest resolution: 2.4 Å / Lowest resolution: 30 Å / Num. obs: 8093 / % possible obs: 91 % / Redundancy: 2.3 % / Num. measured all: 19577 / Rmerge(I) obs: 0.057 |
Reflection shell | *PLUS % possible obs: 91 % / Redundancy: 1.5 % / Num. unique obs: 921 / Rmerge(I) obs: 0.21 / Mean I/σ(I) obs: 3.2 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1O9G Resolution: 2.4→26.44 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.93 / SU B: 10.11 / SU ML: 0.23 / Cross valid method: THROUGHOUT / ESU R: 2.091 / ESU R Free: 0.302 / 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: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 49.48 Å2
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Refinement step | Cycle: LAST / Resolution: 2.4→26.44 Å
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Refine LS restraints |
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