Crystal structure of the Thermus thermophilus (HB8) 30S ribosomal subunit with codon, crystallographically disordered near-cognate transfer RNA anticodon stem-loop mismatched at the second codon position, and streptomycin bound DOI:10.2210/pdb4dr7/pdb   NDB ID: NA1610

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Primary Citation       Related Citations in PDB Entry (REMARK 1) Hide     Molecular Description Hide Classification: Ribosome/antibiotic Structure Weight: 801202.80 Molecule: 16S rRNA Polymer: 1 Type: rna Length: 1522 Chains: A Organism Thermus thermophilus HB8 Molecule: 30S ribosomal protein S2 Polymer: 2 Type: protein Length: 256 Chains: B Organism Thermus thermophilus HB8 Gene Names rpsB rps2 TTHA0861 UniProtKB:   Protein Feature View | Search PDB | P80371     Molecule: 30S ribosomal protein S3 Polymer: 3 Type: protein Length: 239 Chains: C Organism Thermus thermophilus HB8 Gene Names rpsC rps3 TTHA1686 UniProtKB:   Protein Feature View | Search PDB | P80372     Molecule: 30S ribosomal protein S4 Polymer: 4 Type: protein Length: 209 Chains: D Organism Thermus thermophilus HB8 Gene Names rpsD rps4 TTHA1665 UniProtKB:   Protein Feature View | Search PDB | P80373     Molecule: 30S ribosomal protein S5 Polymer: 5 Type: protein Length: 162 Chains: E Organism Thermus thermophilus HB8 Gene Names rpsE TTHA1675 UniProtKB:   Protein Feature View | Search PDB | Q5SHQ5     Molecule: 30S ribosomal protein S6 Polymer: 6 Type: protein Length: 101 Chains: F Organism Thermus thermophilus HB8 Gene Names rpsF TTHA0245 UniProtKB:   Protein Feature View | Search PDB | Q5SLP8     Molecule: 30S ribosomal protein S7 Polymer: 7 Type: protein Length: 156 Chains: G Organism Thermus thermophilus HB8 Gene Names rpsG rps7 TTHA1696 UniProtKB:   Protein Feature View | Search PDB | P17291     Molecule: 30S ribosomal protein S8 Polymer: 8 Type: protein Length: 138 Chains: H Organism Thermus thermophilus HB8 Gene Names rpsH TTHA1678 UniProtKB:   Protein Feature View | Search PDB | Q5SHQ2     Molecule: 30S ribosomal protein S9 Polymer: 9 Type: protein Length: 128 Chains: I Organism Thermus thermophilus HB8 Gene Names rpsI rps9 TTHA1464 UniProtKB:   Protein Feature View | Search PDB | P80374     Molecule: 30S ribosomal protein S10 Polymer: 10 Type: protein Length: 105 Chains: J Organism Thermus thermophilus HB8 Gene Names rpsJ TTHA1693 UniProtKB:   Protein Feature View | Search PDB | Q5SHN7     Molecule: 30S ribosomal protein S11 Polymer: 11 Type: protein Length: 129 Chains: K Organism Thermus thermophilus HB8 Gene Names rpsK rps11 TTHA1666 UniProtKB:   Protein Feature View | Search PDB | P80376     Molecule: 30S ribosomal protein S12 Polymer: 12 Type: protein Length: 135 Chains: L Organism Thermus thermophilus HB8 Gene Names rpsL Ththe16_1715 UniProtKB:   Protein Feature View | Search PDB | F6DEQ7     Molecule: 30S ribosomal protein S13 Polymer: 13 Type: protein Length: 126 Chains: M Organism Thermus thermophilus HB8 Gene Names rpsM rps13 TTHA1667 UniProtKB:   Protein Feature View | Search PDB | P80377     Molecule: 30S ribosomal protein S14 Polymer: 14 Type: protein Length: 61 Chains: N Organism Thermus thermophilus HB8 Gene Names rpsZ rpsN TTHA1679 UniProtKB:   Protein Feature View | Search PDB | Q5SHQ1     Molecule: 30S ribosomal protein S15 Polymer: 15 Type: protein Length: 89 Chains: O Organism Thermus thermophilus HB8 Gene Names rpsO TTHA1138 UniProtKB:   Protein Feature View | Search PDB | Q5SJ76     Molecule: 30S ribosomal protein S16 Polymer: 16 Type: protein Length: 88 Chains: P Organism Thermus thermophilus HB8 Gene Names rpsP TTHA1035 UniProtKB:   Protein Feature View | Search PDB | Q5SJH3     Molecule: 30S ribosomal protein S17 Polymer: 17 Type: protein Length: 105 Chains: Q Organism Thermus thermophilus HB8 Gene Names rpsQ TTHA1683 UniProtKB:   Protein Feature View | Search PDB | Q5SHP7     Molecule: 30S ribosomal protein S18 Polymer: 18 Type: protein Length: 88 Chains: R Organism Thermus thermophilus HB8 Gene Names rpsR TTHA0243 UniProtKB:   Protein Feature View | Search PDB | Q5SLQ0     Molecule: 30S ribosomal protein S19 Polymer: 19 Type: protein Length: 93 Chains: S Organism Thermus thermophilus HB8 Gene Names rpsS TTHA1688 UniProtKB:   Protein Feature View | Search PDB | Q5SHP2     Molecule: 30S ribosomal protein S20 Polymer: 20 Type: protein Length: 106 Chains: T Organism Thermus thermophilus HB8 Gene Names rpsT rps20 TTHA1397 UniProtKB:   Protein Feature View | Search PDB | P80380     Molecule: 30S ribosomal protein THX Polymer: 21 Type: protein Length: 27 Chains: U Organism Thermus thermophilus HB8 Gene Names rpsU TTHA1396 UniProtKB:   Protein Feature View | Search PDB | Q5SIH3     Molecule: 5'-R(*UP*UP*UP*U)-3' Polymer: 22 Type: rna Length: 4 Chains: V Details: mRNA A site Organism Thermus thermophilus HB8 Molecule: 5'-R(*GP*CP*CP*UP*GP*GP*AP*AP*AP*GP*(PSU))-3' Polymer: 23 Type: rna Length: 11 Chains: W Details: ASL (Serine) A site Organism Thermus thermophilus HB8 Molecule: 5'-R(P*UP*GP*GP*AP*AP*AP*GP*(PSU))-3' Polymer: 24 Type: rna Length: 8 Chains: a Details: ASL (Serine) Shine Dalgarno mini helix Organism Thermus thermophilus HB8 Molecule: 5'-R(P*UP*UP*U)-3' Polymer: 25 Type: rna Length: 3 Chains: b Details: mRNA P site Organism Thermus thermophilus HB8     Source Hide Polymer: 1 Scientific Name: Thermus thermophilus   Taxonomy     Polymer: 2 Scientific Name: Thermus thermophilus   Taxonomy     Polymer: 3 Scientific Name: Thermus thermophilus   Taxonomy     Polymer: 4 Scientific Name: Thermus thermophilus   Taxonomy     Polymer: 5 Scientific Name: Thermus thermophilus   Taxonomy     Polymer: 6 Scientific Name: Thermus thermophilus   Taxonomy     Polymer: 7 Scientific Name: Thermus thermophilus   Taxonomy     Polymer: 8 Scientific Name: Thermus thermophilus   Taxonomy     Polymer: 9 Scientific Name: Thermus thermophilus   Taxonomy     Polymer: 10 Scientific Name: Thermus thermophilus   Taxonomy     Polymer: 11 Scientific Name: Thermus thermophilus   Taxonomy     Polymer: 12 Scientific Name: Thermus thermophilus   Taxonomy     Polymer: 13 Scientific Name: Thermus thermophilus   Taxonomy     Polymer: 14 Scientific Name: Thermus thermophilus   Taxonomy     Polymer: 15 Scientific Name: Thermus thermophilus   Taxonomy     Polymer: 16 Scientific Name: Thermus thermophilus   Taxonomy     Polymer: 17 Scientific Name: Thermus thermophilus   Taxonomy     Polymer: 18 Scientific Name: Thermus thermophilus   Taxonomy     Polymer: 19 Scientific Name: Thermus thermophilus   Taxonomy     Polymer: 20 Scientific Name: Thermus thermophilus   Taxonomy     Polymer: 21 Scientific Name: Thermus thermophilus   Taxonomy     Polymer: 22 Scientific Name: Thermus thermophilus   Taxonomy     Polymer: 23 Scientific Name: Thermus thermophilus   Taxonomy     Polymer: 24 Scientific Name: Thermus thermophilus   Taxonomy     Polymer: 25 Scientific Name: Thermus thermophilus   Taxonomy         Related PDB Entries Hide Identifier Details 4DR1    4DR2    4DR3    4DR4    4DR5    4DR6        Ligand Chemical Component Hide Identifier Formula Name Interactions MG Search  Download  Mg MAGNESIUM ION   Ligand Explorer SRY Search  Download  C21 H39 N7 O12 STREPTOMYCIN   Ligand Explorer ZN Search  Download  Zn ZINC ION   Ligand Explorer     Modified Residues Hide Identifier Formula Parent Type PSU Search  C9 H13 N2 O9 P U rnaLinking 7MG Search  C11 H18 N5 O8 P G rnaLinking M2G Search  C12 H18 N5 O8 P G rnaLinking 5MC Search  C10 H16 N3 O8 P C rnaLinking 2MG Search  C11 H16 N5 O8 P G rnaLinking 4OC Search  C11 H18 N3 O8 P C rnaLinking UR3 Search  C10 H15 N2 O9 P U rnaLinking MA6 Search  C12 H18 N5 O7 P A rnaLinking 0TD Search  C5 H9 N O4 S ASP lPeptideLinking     External Domain Annotations Hide Pfam Classification: 22 Domains - data from Pfam   GO Terms: 150 Terms - data from GO      Structural Biology Knowledgebase Data Hide   Nucleic Acid Database Hide View the NDB ID associated with this structure: NA1610     Data in orange boxes are gathered from external resources (when available). 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Biological Assembly            View in 3D More Images... Biological assembly 1 assigned by authors Downloadable viewers: Simple Viewer Protein Workshop Ligand Explorer Kiosk Viewer Other Viewers  KiNG WebMol QuickPDB FirstGlance         MyPDB Personal Annotations Hide     Deposition Summary Hide Authors:   Demirci, H.,  Murphy IV, F.,  Murphy, E.,  Gregory, S.T.,  Dahlberg, A.E.,  Jogl, G. Deposition:   2012-02-16 Release:   2012-11-14 Last Modified (REVDAT):   2013-01-30     Revision History    Hide Mouse over text for details 2013-01-30 Citation 2013-01-23 Citation     Experimental Details Hide Method:   X-RAY DIFFRACTION Exp. Data:   Structure Factors Resolution[Å]:   3.75 R-Value: 0.151 (obs.) R-Free: 0.201 Space Group: P 41 21 2 Unit Cell:   Length [Å] Angles [°] a = 402.49 α = 90.00  b = 402.49 β = 90.00  c = 174.79 γ = 90.00      Molecule of the Month Hide Ribosomal Subunits Ribosome Aminoglycoside Antibiotics Transfer-Messenger RNA