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Yorodumi- PDB-1yjw: Crystal Structure Of Quinupristin Bound To The G2099A Mutant 50S ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1yjw | ||||||||||||
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Title | Crystal Structure Of Quinupristin Bound To The G2099A Mutant 50S Ribosomal Subunit Of Haloarcula Marismortui | ||||||||||||
Components |
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Keywords | RIBOSOME/ANTIBIOTIC / QUINUPRISTIN / DALFOPRISTIN / STREPTOGRAMIN / ANTIBIOTIC / MUTATED 50S SUBUNITS / RIBOSOME / RIBOSOME-ANTIBIOTIC COMPLEX | ||||||||||||
Function / homology | Function and homology information ribonuclease P activity / tRNA 5'-leader removal / box C/D methylation guide snoRNP complex / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of LSU-rRNA / ribosomal large subunit biogenesis / maturation of SSU-rRNA / small-subunit processome / mRNA splicing, via spliceosome / 5S rRNA binding ...ribonuclease P activity / tRNA 5'-leader removal / box C/D methylation guide snoRNP complex / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of LSU-rRNA / ribosomal large subunit biogenesis / maturation of SSU-rRNA / small-subunit processome / mRNA splicing, via spliceosome / 5S rRNA binding / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / cytoplasmic translation / tRNA binding / negative regulation of translation / rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / nucleotide binding / DNA repair / mRNA binding / DNA binding / zinc ion binding Similarity search - Function | ||||||||||||
Biological species | Haloarcula marismortui (Halophile) Streptomyces graminofaciens (bacteria) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å | ||||||||||||
Authors | Tu, D. / Blaha, G. / Moore, P.B. / Steitz, T.A. | ||||||||||||
Citation | Journal: Cell(Cambridge,Mass.) / Year: 2005 Title: Structures of Mlsbk Antibiotics Bound to Mutated Large Ribosomal Subunits Provide a Structural Explanation for Resistance. Authors: Tu, D. / Blaha, G. / Moore, P.B. / Steitz, T.A. | ||||||||||||
History |
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Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "KC" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "KC" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 5-STRANDED BARREL THIS IS REPRESENTED BY A 6-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1yjw.cif.gz | 2.5 MB | Display | PDBx/mmCIF format |
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PDB format | pdb1yjw.ent.gz | 1.9 MB | Display | PDB format |
PDBx/mmJSON format | 1yjw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yj/1yjw ftp://data.pdbj.org/pub/pdb/validation_reports/yj/1yjw | HTTPS FTP |
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-Related structure data
Related structure data | 1yhqC 1yi2C 1yijC 1yitC 1yj9C 1yjnC 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
-RNA chain , 2 types, 2 molecules 09
#1: RNA chain | Mass: 946141.375 Da / Num. of mol.: 1 / Mutation: YES / Source method: isolated from a natural source / Details: ENCODED BY RRNA OPERON / Source: (natural) Haloarcula marismortui (Halophile) / Strain: DT41 / References: GenBank: 55229667 |
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#6: RNA chain | Mass: 39303.402 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Haloarcula marismortui (Halophile) / Strain: DT41 / References: GenBank: 43619 |
+50S ribosomal protein ... , 29 types, 29 molecules 123ABCDEFGHIJKLMNOPQRSTUVWXYZ
-Protein/peptide , 1 types, 1 molecules 4
#5: Protein/peptide | Mass: 1024.236 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Streptomyces graminofaciens (bacteria) |
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-Non-polymers , 6 types, 8042 molecules
#33: Chemical | ChemComp-MG / #34: Chemical | #35: Chemical | ChemComp-NA / #36: Chemical | ChemComp-CL / #37: Chemical | ChemComp-CD / #38: Water | ChemComp-HOH / | |
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-Details
Compound details | QUINUPRISTSequence details | SEQUENCE SEQUENCE REFERENCE FOR THIS RIBOSOME: BALIGA, N.S., BONNEAU, R., FACCIOTTI, M.T., PAN, M., ...SEQUENCE SEQUENCE REFERENCE FOR THIS RIBOSOME: BALIGA, N.S., BONNEAU, R., FACCIOTTI, M.T., PAN, M., GLUSMAN, G., DEUTSCH, E.W., SHANNON, P., CHIU, Y., WENG, R.S., GAN, R.R., ET AL.(2004) . GENOME SEQUENCE OF HALOARCULA | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.1 Å3/Da / Density % sol: 60 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 5.8 Details: PEG 6000, KCL, NH4CL, MGCL2, KACETATE, PH 5.8, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 292K | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 9, 2004 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 3→50 Å / Num. obs: 330497 / Redundancy: 4.7 % / Biso Wilson estimate: 70.5 Å2 / Rmerge(I) obs: 0.132 / Net I/σ(I): 9.4 |
Reflection shell | Resolution: 3→3.11 Å / Rmerge(I) obs: 0.618 / Mean I/σ(I) obs: 1.9 / % possible all: 92.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→29.98 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 186612.58 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 Details: REFLECTION DATA IS REPORTED TO RESOLUTION HIGH OF 3.00, BUT REFINEMENT DATA IS REPORTED TO RESOLUTION HIGH OF 2.90. THIS IS BECAUSE ALL DATA WERE USED IN REFINEMENT (I.E. INCLUDING DATA THAT ...Details: REFLECTION DATA IS REPORTED TO RESOLUTION HIGH OF 3.00, BUT REFINEMENT DATA IS REPORTED TO RESOLUTION HIGH OF 2.90. THIS IS BECAUSE ALL DATA WERE USED IN REFINEMENT (I.E. INCLUDING DATA THAT HAVE I/SIGMA WEAKER THAN 2.0).
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 32.33 Å2 / ksol: 0.31 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 50.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.9→29.98 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.9→3.08 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
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Xplor file |
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