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Yorodumi- PDB-1p91: Crystal Structure of RlmA(I) enzyme: 23S rRNA n1-G745 methyltrans... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1p91 | ||||||
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Title | Crystal Structure of RlmA(I) enzyme: 23S rRNA n1-G745 methyltransferase (NORTHEAST STRUCTURAL GENOMICS CONSORTIUM TARGET ER19) | ||||||
Components | Ribosomal RNA large subunit methyltransferase A | ||||||
Keywords | TRANSFERASE / RlmA / RrmA / methyltransferase / G745 / ER19 / 23S rRNA / NESG / STRUCTURAL GENOMICS / PSI / Protein Structure Initiative / Northeast Structural Genomics Consortium | ||||||
Function / homology | Function and homology information 23S rRNA (guanine745-N1)-methyltransferase / 23S rRNA (guanine(745)-N(1))-methyltransferase activity / rRNA (guanine-N1-)-methyltransferase activity / rRNA base methylation / methyltransferase activity / zinc ion binding Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.8 Å | ||||||
Authors | Das, K. / Acton, T. / Montelione, G. / Arnold, E. / Northeast Structural Genomics Consortium (NESG) | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.Usa / Year: 2004 Title: Crystal structure of RlmAI: implications for understanding the 23S rRNA G745/G748-methylation at the macrolide antibiotic-binding site. Authors: Das, K. / Acton, T. / Chiang, Y. / Shih, L. / Arnold, E. / Montelione, G.T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1p91.cif.gz | 116.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1p91.ent.gz | 96.4 KB | Display | PDB format |
PDBx/mmJSON format | 1p91.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p9/1p91 ftp://data.pdbj.org/pub/pdb/validation_reports/p9/1p91 | HTTPS FTP |
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-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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Unit cell |
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Details | The biological assembly is a dimer. One monomers is related to the other by ~159 degree rotation about the NCS axis. |
-Components
#1: Protein | Mass: 30788.188 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: RRMA OR B1822 / Production host: Escherichia coli (E. coli) / References: UniProt: P36999, EC: 2.1.1.51 #2: Chemical | #3: Chemical | ChemComp-SO4 / #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 3.81 Å3/Da / Density % sol: 67.68 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 300 K / Method: vapor diffusion / pH: 6.5 Details: Ammonium sulfate, Lithium Sulfate, pH 6.5, VAPOR DIFFUSION, temperature 300K | ||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7.5 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction |
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Diffraction source |
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Detector |
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Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2.8→50 Å / Num. all: 21876 / Num. obs: 21876 / % possible obs: 93 % / Observed criterion σ(I): -0.5 / Biso Wilson estimate: 41.8 Å2 / Rmerge(I) obs: 0.106 / Net I/σ(I): 11 | |||||||||||||||
Reflection shell | Resolution: 2.8→2.85 Å / % possible all: 80.2 | |||||||||||||||
Reflection | *PLUS Lowest resolution: 50 Å / % possible obs: 93 % / Num. measured all: 88268 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.8→20 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 2974439.24 / Data cutoff high rms absF: 2974439.24 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 1 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 10 Å2 / ksol: 0.251692 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 55.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.8→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.8→2.97 Å / Rfactor Rfree error: 0.035 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Highest resolution: 2.8 Å / Lowest resolution: 20 Å / % reflection Rfree: 5 % | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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