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Yorodumi- PDB-1k8a: Co-crystal structure of Carbomycin A bound to the 50S ribosomal s... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1k8a | ||||||
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Title | Co-crystal structure of Carbomycin A bound to the 50S ribosomal subunit of Haloarcula marismortui | ||||||
Components |
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Keywords | RIBOSOME / antibiotic / carbomycin A / macrolide | ||||||
Function / homology | Function and homology information ribonuclease P activity / tRNA 5'-leader removal / cytosolic ribosome / large ribosomal subunit rRNA binding / large ribosomal subunit / ribosome biogenesis / 5S rRNA binding / cytosolic large ribosomal subunit / tRNA binding / rRNA binding ...ribonuclease P activity / tRNA 5'-leader removal / cytosolic ribosome / large ribosomal subunit rRNA binding / large ribosomal subunit / ribosome biogenesis / 5S rRNA binding / cytosolic large ribosomal subunit / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / nucleotide binding / DNA repair / DNA binding / zinc ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Haloarcula marismortui (Halophile) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å | ||||||
Authors | Hansen, J.L. / Ippolito, J.A. / Ban, N. / Nissen, P. / Moore, P.B. / Steitz, T. | ||||||
Citation | Journal: Mol.Cell / Year: 2002 Title: The structures of four macrolide antibiotics bound to the large ribosomal subunit. Authors: Hansen, J.L. / Ippolito, J.A. / Ban, N. / Nissen, P. / Moore, P.B. / Steitz, T.A. #1: Journal: Science / Year: 2000 Title: The complete atomic structure of the large ribosomal subunit at 2.4 A resolution Authors: Ban, N. / Nissen, P. / Hansen, J. / Moore, P.B. / Steitz, T.A. #2: Journal: Science / Year: 2000 Title: The structural basis of ribosome activity in peptide bond synthesis Authors: Nissen, P. / Hansen, J. / Ban, N. / Moore, P.B. / Steitz, T.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1k8a.cif.gz | 2.5 MB | Display | PDBx/mmCIF format |
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PDB format | pdb1k8a.ent.gz | 1.9 MB | Display | PDB format |
PDBx/mmJSON format | 1k8a.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k8/1k8a ftp://data.pdbj.org/pub/pdb/validation_reports/k8/1k8a | HTTPS FTP |
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-Related structure data
Related structure data | 1k9mC 1kd1C 1m1kC 1jj2S C: citing same article (ref.) S: Starting model for refinement |
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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 AB
#1: RNA chain | Mass: 946034.375 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Haloarcula marismortui (Halophile) / References: GenBank: 3377779 |
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#2: RNA chain | Mass: 39318.414 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Haloarcula marismortui (Halophile) / References: GenBank: 3377779 |
+RIBOSOMAL PROTEIN ... , 28 types, 28 molecules CDEFGHIJKLMNOPQRSTUVWXYZ1234
-Non-polymers , 7 types, 8084 molecules
#31: Chemical | ChemComp-CAI / | ||||||||||
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#32: Chemical | ChemComp-MG / #33: Chemical | ChemComp-NA / #34: Chemical | ChemComp-CL / #35: Chemical | #36: Chemical | ChemComp-CD / #37: 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: 3.17 Å3/Da / Density % sol: 61.17 % | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, sitting drop / pH: 5.8 Details: PEG 6K, KCl, NH4Cl, KOAc MgCl2, pH 5.8, VAPOR DIFFUSION, SITTING DROP, temperature 292K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS pH: 7.1 / Method: back-extraction, vapor diffusion / Details: Ban, N., (2000) Science, 289, 905. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1.033 Å |
Detector | Type: CUSTOM-MADE / Detector: CCD / Date: Sep 27, 2000 |
Radiation | Monochromator: Si 111 Si 220 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.033 Å / Relative weight: 1 |
Reflection | Resolution: 3→50 Å / Num. all: 370864 / Num. obs: 367880 / % possible obs: 99.2 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 7.2 % / Biso Wilson estimate: 44 Å2 / Rmerge(I) obs: 0.136 / Rsym value: 0.136 / Net I/σ(I): 14.2 |
Reflection shell | Resolution: 2.98→3.09 Å / Redundancy: 34384 % / Rmerge(I) obs: 0.816 / Mean I/σ(I) obs: 2 / Num. unique all: 36270 / Rsym value: 0.816 / % possible all: 94.8 |
Reflection | *PLUS % possible obs: 93.3 % / Redundancy: 6.8 % / Rmerge(I) obs: 0.132 |
Reflection shell | *PLUS Highest resolution: 3 Å / Lowest resolution: 3.1 Å / % possible obs: 80.2 % / Rmerge(I) obs: 0.68 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1JJ2 native 50S subunit Resolution: 3→20 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 270687.51 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 Stereochemistry target values: RNA from CNS Brunger, Berman modified by Sjoerd Protein from CNS protein_rep.param Carbomycin A constructed from CSD files DMCLM10, NAVTAF, PVVBDM01, using xplo2d
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 30.6577 Å2 / ksol: 0.291887 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 58.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3→3.11 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 10
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Xplor file |
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Refinement | *PLUS Highest resolution: 3 Å / Lowest resolution: 20 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Highest resolution: 3 Å / Lowest resolution: 3.1 Å |