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Yorodumi- PDB-1qao: THE STRUCTURE OF THE RRNA METHYLTRANSFERASE ERMC': IMPLICATIONS F... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1qao | ||||||
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Title | THE STRUCTURE OF THE RRNA METHYLTRANSFERASE ERMC': IMPLICATIONS FOR THE REACTION MECHANISM | ||||||
Components | ERMC' METHYLTRANSFERASE | ||||||
Keywords | TRANSFERASE / BINARY COMPLEX WITH S-ADENOSYLMETHIONINE | ||||||
Function / homology | Function and homology information 23S rRNA (adenine2085-N6)-dimethyltransferase / 23S rRNA (adenine(2085)-N(6))-dimethyltransferase activity / rRNA (adenine-N6,N6-)-dimethyltransferase activity / response to antibiotic / RNA binding / cytosol Similarity search - Function | ||||||
Biological species | Bacillus subtilis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.7 Å | ||||||
Authors | Schluckebier, G. / Zhong, P. / Stewart, K.D. / Kavanaugh, T.J. / Abad-Zapatero, C. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 1999 Title: The 2.2 A structure of the rRNA methyltransferase ErmC' and its complexes with cofactor and cofactor analogs: implications for the reaction mechanism. Authors: Schluckebier, G. / Zhong, P. / Stewart, K.D. / Kavanaugh, T.J. / Abad-Zapatero, C. #1: Journal: Biochemistry / Year: 1998 Title: Crystal structure of ErmC', an RNA methyltransferase which mediates antibiotic resistance in bacteria Authors: Bussiere, D.E. / Muchmore, S.W. / Dealwis, C.G. / Schluckebier, G. / Nienaber, V.L. / Edalji, R.P. / Walter, K.A. / Ladror, U.S. / Holzman, T.F. / Abad-Zapatero, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1qao.cif.gz | 60.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1qao.ent.gz | 44.7 KB | Display | PDB format |
PDBx/mmJSON format | 1qao.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1qao_validation.pdf.gz | 441.9 KB | Display | wwPDB validaton report |
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Full document | 1qao_full_validation.pdf.gz | 445.7 KB | Display | |
Data in XML | 1qao_validation.xml.gz | 7 KB | Display | |
Data in CIF | 1qao_validation.cif.gz | 9.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qa/1qao ftp://data.pdbj.org/pub/pdb/validation_reports/qa/1qao | 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: 28955.529 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis (bacteria) / Production host: Escherichia coli (E. coli) / Strain (production host): BD1109 / References: UniProt: P13956, EC: 2.1.1.48 |
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#2: Chemical | ChemComp-SAM / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.48 Å3/Da / Density % sol: 64.67 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.8 Details: PEG 8000, ammonium acetate, pH 7.8 at 298 K, VAPOR DIFFUSION, HANGING DROP | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS 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 RU200 / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Jun 11, 1997 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→50 Å / Num. all: 11313 / Num. obs: 11313 / % possible obs: 95.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Biso Wilson estimate: 68 Å2 / Rmerge(I) obs: 0.039 / Net I/σ(I): 15.1 |
Reflection shell | Resolution: 2.7→2.8 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.298 / Num. unique all: 1113 / % possible all: 96.6 |
Reflection | *PLUS Num. measured all: 36172 |
Reflection shell | *PLUS % possible obs: 96.6 % / Mean I/σ(I) obs: 4.4 |
-Processing
Software |
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Refinement | Resolution: 2.7→50 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.7→50 Å
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Refine LS restraints |
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Software | *PLUS Name: CNS / Classification: refinement | |||||||||||||||
Refinement | *PLUS Highest resolution: 2.7 Å / Lowest resolution: 50 Å / σ(F): 0 / Rfactor obs: 0.23 / Rfactor Rwork: 0.23 | |||||||||||||||
Solvent computation | *PLUS | |||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||
Refine LS restraints | *PLUS
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