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Yorodumi- PDB-1qam: THE STRUCTURE OF THE RRNA METHYLTRANSFERASE ERMC': IMPLICATIONS F... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1qam | ||||||
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Title | THE STRUCTURE OF THE RRNA METHYLTRANSFERASE ERMC': IMPLICATIONS FOR THE REACTION MECHANISM | ||||||
Components | ERMC' METHYLTRANSFERASE | ||||||
Keywords | TRANSFERASE / RRNA METHYLTRANSFERASE ERMC' / COFACTOR ANALOGS | ||||||
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: 2.2 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 | 1qam.cif.gz | 64.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1qam.ent.gz | 47.6 KB | Display | PDB format |
PDBx/mmJSON format | 1qam.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1qam_validation.pdf.gz | 378 KB | Display | wwPDB validaton report |
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Full document | 1qam_full_validation.pdf.gz | 379.7 KB | Display | |
Data in XML | 1qam_validation.xml.gz | 6.3 KB | Display | |
Data in CIF | 1qam_validation.cif.gz | 9.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qa/1qam ftp://data.pdbj.org/pub/pdb/validation_reports/qa/1qam | 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) / References: UniProt: P13956, EC: 2.1.1.48 | ||
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#2: Chemical | #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.49 Å3/Da / Density % sol: 64.79 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
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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: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 1, 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: 2.2→50 Å / Num. all: 20680 / Num. obs: 20680 / % possible obs: 96 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Biso Wilson estimate: 42 Å2 / Rmerge(I) obs: 0.054 / Net I/σ(I): 17 |
Reflection shell | Resolution: 2.2→2.28 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.308 / % possible all: 94.4 |
Reflection | *PLUS % possible obs: 96 % / Num. measured all: 72558 |
Reflection shell | *PLUS % possible obs: 94.4 % / Mean I/σ(I) obs: 4.4 |
-Processing
Software |
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Refinement | Resolution: 2.2→50 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ENGH & HUBER
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Refinement step | Cycle: LAST / Resolution: 2.2→50 Å
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Refine LS restraints |
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Software | *PLUS Name: CNS / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.2 Å / Lowest resolution: 50 Å / σ(F): 0 / Rfactor obs: 0.221 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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