+Open data
-Basic information
Entry | Database: PDB / ID: 4v90 | |||||||||
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Title | Thermus thermophilus Ribosome | |||||||||
Components |
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Keywords | RIBOSOME / TRANSLOCATION / GTPASE ACTIVATION ROTATION | |||||||||
Function / homology | Function and homology information ribosome disassembly / endo-alpha-N-acetylgalactosaminidase activity / Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds / translation elongation factor activity / large ribosomal subunit / regulation of translation / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding ...ribosome disassembly / endo-alpha-N-acetylgalactosaminidase activity / Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds / translation elongation factor activity / large ribosomal subunit / regulation of translation / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / transferase activity / 5S rRNA binding / large ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / cytosolic large ribosomal subunit / cytoplasmic translation / tRNA binding / rRNA binding / negative regulation of translation / ribosome / structural constituent of ribosome / translation / ribonucleoprotein complex / GTPase activity / mRNA binding / GTP binding / zinc ion binding / metal ion binding / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | THERMUS THERMOPHILUS HB8 (bacteria) synthetic construct (others) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.95 Å | |||||||||
Authors | Chen, Y. / Feng, S. / Kumar, V. / Ero, R. / Gao, Y.G. | |||||||||
Citation | Journal: Nat. Struct. Mol. Biol. / Year: 2013 Title: Structure of EF-G-ribosome complex in a pretranslocation state. Authors: Chen, Y. / Feng, S. / Kumar, V. / Ero, R. / Gao, Y.G. | |||||||||
History |
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Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "QA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "QA" 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. SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4v90.cif.gz | 3.8 MB | Display | PDBx/mmCIF format |
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PDB format | pdb4v90.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 4v90.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4v90_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 4v90_full_validation.pdf.gz | 2.6 MB | Display | |
Data in XML | 4v90_validation.xml.gz | 492.8 KB | Display | |
Data in CIF | 4v90_validation.cif.gz | 692.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v9/4v90 ftp://data.pdbj.org/pub/pdb/validation_reports/v9/4v90 | HTTPS FTP |
-Related structure data
Related structure data | 2wri 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 , 5 types, 5 molecules AAAVAXBABB
#1: RNA chain | Mass: 493040.812 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS HB8 (bacteria) / Strain: MRC-MSAW1 / References: GenBank: 48256 |
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#22: RNA chain | Mass: 24484.555 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS HB8 (bacteria) / Strain: MRC-MSAW1 |
#23: RNA chain | Mass: 2840.750 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#35: RNA chain | Mass: 947959.500 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS HB8 (bacteria) / Strain: MRC-MSAW1 / References: GenBank: 55771382 |
#36: RNA chain | Mass: 39540.617 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS HB8 (bacteria) / Strain: MRC-MSAW1 / References: GenBank: 55979969 |
-30S RIBOSOMAL PROTEIN ... , 20 types, 20 molecules ABACADAEAFAGAHAIAJAKALAMANAOAPAQARASATAU
#2: Protein | Mass: 29317.703 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS HB8 (bacteria) / Strain: MRC-MSAW1 / References: UniProt: P80371 |
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#3: Protein | Mass: 26751.076 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS HB8 (bacteria) / Strain: MRC-MSAW1 / References: UniProt: P80372 |
#4: Protein | Mass: 24373.447 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS HB8 (bacteria) / Strain: MRC-MSAW1 / References: UniProt: P80373 |
#5: Protein | Mass: 17583.416 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS HB8 (bacteria) / Strain: MRC-MSAW1 / References: UniProt: Q5SHQ5 |
#6: Protein | Mass: 11988.753 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS HB8 (bacteria) / Strain: MRC-MSAW1 / References: UniProt: Q5SLP8 |
#7: Protein | Mass: 18050.973 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS HB8 (bacteria) / Strain: MRC-MSAW1 / References: UniProt: P17291 |
#8: Protein | Mass: 15868.570 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS HB8 (bacteria) / Strain: MRC-MSAW1 / References: UniProt: Q5SHQ2, UniProt: A0A0M9AFS9*PLUS |
#9: Protein | Mass: 14410.614 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS HB8 (bacteria) / Strain: MRC-MSAW1 / References: UniProt: P80374 |
#10: Protein | Mass: 11954.968 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS HB8 (bacteria) / Strain: MRC-MSAW1 / References: UniProt: Q5SHN7 |
#11: Protein | Mass: 13737.868 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS HB8 (bacteria) / Strain: MRC-MSAW1 / References: UniProt: P80376 |
#12: Protein | Mass: 14637.384 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS HB8 (bacteria) / Strain: MRC-MSAW1 / References: UniProt: Q5SHN3 |
#13: Protein | Mass: 14338.861 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS HB8 (bacteria) / Strain: MRC-MSAW1 / References: UniProt: P80377 |
#14: Protein | Mass: 7158.725 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS HB8 (bacteria) / Strain: MRC-MSAW1 / References: UniProt: Q5SHQ1, UniProt: A0A0N0BLP2*PLUS |
#15: Protein | Mass: 10578.407 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS HB8 (bacteria) / Strain: MRC-MSAW1 / References: UniProt: Q5SJ76 |
#16: Protein | Mass: 10409.983 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS HB8 (bacteria) / Strain: MRC-MSAW1 / References: UniProt: Q5SJH3 |
#17: Protein | Mass: 12325.655 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS HB8 (bacteria) / Strain: MRC-MSAW1 / References: UniProt: Q5SHP7, UniProt: A0A0N0BLS5*PLUS |
#18: Protein | Mass: 10258.299 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS HB8 (bacteria) / Strain: MRC-MSAW1 / References: UniProt: Q5SLQ0 |
#19: Protein | Mass: 10605.464 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS HB8 (bacteria) / Strain: MRC-MSAW1 / References: UniProt: Q5SHP2 |
#20: Protein | Mass: 11736.143 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS HB8 (bacteria) / Strain: MRC-MSAW1 / References: UniProt: P80380 |
#21: Protein/peptide | Mass: 3350.030 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS HB8 (bacteria) / Strain: MRC-MSAW1 / References: UniProt: Q5SIH3 |
-Protein , 5 types, 5 molecules AYBCBJBKBL
#24: Protein | Mass: 76977.102 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS HB8 (bacteria) / Strain: MRC-MSAW1 / References: UniProt: Q5SHN5 |
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#37: Protein | Mass: 24741.523 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS HB8 (bacteria) / Strain: MRC-MSAW1 / References: UniProt: Q5SLP7 |
#43: Protein | Mass: 11109.704 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS HB8 (bacteria) / Strain: MRC-MSAW1 |
#44: Protein | Mass: 11932.701 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS HB8 (bacteria) / Strain: MRC-MSAW1 |
#45: Protein | Mass: 6060.462 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS HB8 (bacteria) / Strain: MRC-MSAW1 |
+50S RIBOSOMAL PROTEIN ... , 28 types, 28 molecules B0B1B2B3B4B5B6B7B8B9BDBEBFBGBHBNBOBPBQBRBSBTBUBVBWBXBYBZ
-Non-polymers , 4 types, 529 molecules
#59: Chemical | ChemComp-MG / #60: Chemical | #61: Chemical | ChemComp-GCP / | #62: 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: 3.25 Å3/Da / Density % sol: 62.19 % / Description: NONE |
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Crystal grow | pH: 6.5 Details: 0.1M MES PH 6.5, 5.8-6.8%PEG20K, 30-120 MM KCL AND 0.8-2.5% GLYCEROL |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 27, 2013 / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.95→50 Å / Num. obs: 617945 / % possible obs: 100 % / Observed criterion σ(I): 1.6 / Redundancy: 7.2 % / Biso Wilson estimate: 48.2 Å2 / Rmerge(I) obs: 0.26 / Net I/σ(I): 8 |
Reflection shell | Resolution: 2.95→3.05 Å / Redundancy: 6.3 % / Rmerge(I) obs: 1.15 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2WRI 2wri Resolution: 2.95→49.75 Å / Rfactor Rfree error: 0.001 / Data cutoff high absF: 10834194.3 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 22.2545 Å2 / ksol: 0.3 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 58.5 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.95→49.75 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: NONE | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.95→3.13 Å / Rfactor Rfree error: 0.005 / Total num. of bins used: 6
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Xplor file |
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