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Yorodumi- PDB-2zjp: Thiopeptide antibiotic Nosiheptide bound to the large ribosomal s... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2zjp | |||||||||
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Title | Thiopeptide antibiotic Nosiheptide bound to the large ribosomal subunit of Deinococcus radiodurans | |||||||||
Components |
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Keywords | RIBOSOME/ANTIBIOTIC / NOSIHEPTIDE / THIOPEPTIDE / THIAZOLE / ANTIBIOTIC / L11 / S50 / ANTIBACTERIAL / RIBOSOME-ANTIBIOTIC COMPLEX / RIBOSOME / ZINC-FINGER / TRANSLATION REGULATION / RNA-BINDING | |||||||||
Function / homology | Function and homology information negative regulation of translational elongation / large ribosomal subunit / transferase activity / 5S rRNA binding / large ribosomal subunit rRNA binding / defense response to Gram-negative bacterium / cytosolic large ribosomal subunit / cytoplasmic translation / tRNA binding / rRNA binding ...negative regulation of translational elongation / large ribosomal subunit / transferase activity / 5S rRNA binding / large ribosomal subunit rRNA binding / defense response to Gram-negative bacterium / cytosolic large ribosomal subunit / cytoplasmic translation / tRNA binding / rRNA binding / negative regulation of translation / ribosome / defense response to Gram-positive bacterium / structural constituent of ribosome / translation / ribonucleoprotein complex / mRNA binding / RNA binding / metal ion binding / cytoplasm Similarity search - Function | |||||||||
Biological species | DEINOCOCCUS RADIODURANS (radioresistant) STREPTOMYCES ACTUOSUS (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.7 Å | |||||||||
Model type details | CA ATOMS ONLY, CHAIN 1, 2, 3 | |||||||||
Authors | Harms, J.M. / Wilson, D.N. / Schluenzen, F. / Connell, S.R. / Stachelhaus, T. / Zaborowska, Z. / Spahn, C.M.T. / Fucini, P. | |||||||||
Citation | Journal: Mol.Cell / Year: 2008 Title: Translational Regulation Via L11: Molecular Switches on the Ribosome Turned on and Off by Thiostrepton and Micrococcin. Authors: Harms, J.M. / Wilson, D.N. / Schluenzen, F. / Connell, S.R. / Stachelhaus, T. / Zaborowska, Z. / Spahn, C.M. / Fucini, P. | |||||||||
History |
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Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "HA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "HA" 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 | 2zjp.cif.gz | 2.1 MB | Display | PDBx/mmCIF format |
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PDB format | pdb2zjp.ent.gz | 1.6 MB | Display | PDB format |
PDBx/mmJSON format | 2zjp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2zjp_validation.pdf.gz | 792.5 KB | Display | wwPDB validaton report |
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Full document | 2zjp_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 2zjp_validation.xml.gz | 303 KB | Display | |
Data in CIF | 2zjp_validation.cif.gz | 419.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zj/2zjp ftp://data.pdbj.org/pub/pdb/validation_reports/zj/2zjp | HTTPS FTP |
-Related structure data
Related structure data | 2zjqC 2zjrSC 3cf5C 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
+50S RIBOSOMAL PROTEIN ... , 28 types, 28 molecules 1234ABCDEFGHIJKLMNOPQRSTUVWY
-Protein/peptide , 1 types, 1 molecules 5
-RNA chain , 2 types, 2 molecules XZ
#29: RNA chain | Mass: 933405.000 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) DEINOCOCCUS RADIODURANS (radioresistant) / References: GenBank: AE000513 |
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#31: RNA chain | Mass: 39605.695 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) DEINOCOCCUS RADIODURANS (radioresistant) / References: GenBank: AE000513 |
-Non-polymers , 3 types, 38 molecules
#32: Chemical | #33: Chemical | ChemComp-NO1 / | Type: Thiopeptide / Class: Antibiotic / Mass: 205.210 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H11NO3 Details: NOSIHEPTIDE IS A HETROCYCLIC THIOPEPTIDE, CONSISTING OF FIVE THIAZOLES AND ONE 3-HYDROXYPYRIDINE RINGS. A MODIFIED INDOLE RING NO1(14) IS LINKED VIA THE SIDE CHAINS OF 3-HYDROXY 3GL(6) AND ...Details: NOSIHEPTIDE IS A HETROCYCLIC THIOPEPTIDE, CONSISTING OF FIVE THIAZOLES AND ONE 3-HYDROXYPYRIDINE RINGS. A MODIFIED INDOLE RING NO1(14) IS LINKED VIA THE SIDE CHAINS OF 3-HYDROXY 3GL(6) AND CYS(8). THE OBSERVED C-TERMINAL AMINO GROUP NH2(13) IS LIKELY TO BE A POST-TRANSLATIONAL DECARBOXYLATED REMNANT OF A SER C-TERMINAL RESIDUE References: Nosiheptide #34: Chemical | ChemComp-MG / |
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-Details
Compound details | Nosiheptide is a member of a sulphur-rich heterocyclic peptides class. All share a macrocylic core, ...Nosiheptide is a member of a sulphur-rich heterocyclic peptides class. All share a macrocylic core, consisting of a nitrogen containing, six-membered ring central to dehydroamino acids and a subset of five member ring structures including thiazoles, thiazolines and oxazoles. The main characteristic of the nosiheptide structure is a general tendency to be more oxidized than the thiostrepton one. No thiazoline, or hydrogenated quinaldic precursor nor tetrahydropyridine rings are present in nosiheptide. All the corresponding rings are unsaturated. Nosiheptide possess an indolic acid ring system that is appended to the side chains of the Ser/Cys and a central 6-membered nitrogen heterocycle produced by cyclization between two corresponding dehydroalanine acids with incorporation of an adjacent carbonyl group. Thiazole formation is by nucleophilic addition of each Cys side chain to the proceeding carbonyl group followed by dehydration and dehydrogenation. HERE, NOSIHEPTID |
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Nonpolymer details | THE CHIRALITY OF THE 4-HYDROXY GLUTAMIC ACID (3GL) IS NOT SATTELED. IN THE CURRENT ENTRY THE ...THE CHIRALITY OF THE 4-HYDROXY GLUTAMIC ACID (3GL) IS NOT SATTELED. IN THE CURRENT ENTRY THE DIASTEREOM |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 7 |
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-Sample preparation
Crystal | Density Matthews: 4 Å3/Da / Density % sol: 66 % |
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Crystal grow | Details: VAPOR DIFFUSION, HANGING DROP |
-Data collection
Diffraction |
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Detector |
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Radiation |
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Radiation wavelength |
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Reflection | Resolution: 3.7→30 Å / Num. obs: 216249 / % possible obs: 85.6 % / Observed criterion σ(I): 1 / Rsym value: 0.14 / Net I/σ(I): 6.1 | |||||||||||||||
Reflection shell | Resolution: 3.7→3.76 Å / Mean I/σ(I) obs: 1.2 / Rsym value: 0.63 / % possible all: 75.2 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2ZJR Resolution: 3.7→30 Å / σ(F): 2
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Refinement step | Cycle: LAST / Resolution: 3.7→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.3→3.76 Å / % reflection obs: 63 % |