4DV4 Ribosome date Feb 22, 2012
title Crystal Structure Of The Thermus Thermophilus 30s Ribosomal With A 16s Rrna Mutation, A914g
authors H.Demirci, F.Murphy Iv, E.Murphy, S.T.Gregory, A.E.Dahlberg, G.Jo
compound source
Molecule: 16s Rrna
Chain: A
Mutation: Yes
Organism_scientific: Thermus Thermophilus
Organism_taxid: 300852
Strain: Hb8

Molecule: Ribosomal Protein S2
Chain: B

Organism_scientific: Thermus Thermophilus
Organism_taxid: 300852
Strain: Hb8

Molecule: Ribosomal Protein S3
Chain: C

Organism_scientific: Thermus Thermophilus
Organism_taxid: 300852
Strain: Hb8

Molecule: Ribosomal Protein S4
Chain: D

Organism_scientific: Thermus Thermophilus
Organism_taxid: 300852
Strain: Hb8

Molecule: Ribosomal Protein S5
Chain: E

Organism_scientific: Thermus Thermophilus
Organism_taxid: 300852
Strain: Hb8

Molecule: Ribosomal Protein S6
Chain: F

Organism_scientific: Thermus Thermophilus
Organism_taxid: 300852
Strain: Hb8

Molecule: Ribosomal Protein S7
Chain: G

Organism_scientific: Thermus Thermophilus
Organism_taxid: 300852
Strain: Hb8

Molecule: Ribosomal Protein S8
Chain: H

Organism_scientific: Thermus Thermophilus
Organism_taxid: 300852
Strain: Hb8

Molecule: Ribosomal Protein S9
Chain: I

Organism_scientific: Thermus Thermophilus
Organism_taxid: 300852
Strain: Hb8

Molecule: Ribosomal Protein S10
Chain: J

Organism_scientific: Thermus Thermophilus
Organism_taxid: 300852
Strain: Hb8

Molecule: Ribosomal Protein S11
Chain: K

Organism_scientific: Thermus Thermophilus
Organism_taxid: 300852
Strain: Hb8

Molecule: Ribosomal Protein S12
Chain: L

Organism_scientific: Thermus Thermophilus
Organism_taxid: 300852
Strain: Hb8

Molecule: Ribosomal Protein S13
Chain: M

Organism_scientific: Thermus Thermophilus
Organism_taxid: 300852
Strain: Hb8

Molecule: Ribosomal Protein S14
Chain: N

Organism_scientific: Thermus Thermophilus
Organism_taxid: 300852
Strain: Hb8

Molecule: Ribosomal Protein S15
Chain: O

Organism_scientific: Thermus Thermophilus
Organism_taxid: 300852
Strain: Hb8

Molecule: Ribosomal Protein S16
Chain: P

Organism_scientific: Thermus Thermophilus
Organism_taxid: 300852
Strain: Hb8

Molecule: Ribosomal Protein S17
Chain: Q

Organism_scientific: Thermus Thermophilus
Organism_taxid: 300852
Strain: Hb8

Molecule: Ribosomal Protein S18
Chain: R

Organism_scientific: Thermus Thermophilus
Organism_taxid: 300852
Strain: Hb8

Molecule: Ribosomal Protein S19
Chain: S

Organism_scientific: Thermus Thermophilus
Organism_taxid: 300852
Strain: Hb8

Molecule: Ribosomal Protein S20
Chain: T

Organism_scientific: Thermus Thermophilus
Organism_taxid: 300852
Strain: Hb8

Molecule: Ribosomal Protein Thx
Chain: U

Organism_scientific: Thermus Thermophilus
Organism_taxid: 300852
Strain: Hb8
symmetry Space Group: P 41 21 2
R_factor 0.153 R_Free 0.208
crystal
cell
length a length b length c angle alpha angle beta angle gamma
402.638 402.638 174.747 90.00 90.00 90.00
method X-Ray Diffractionresolution 3.65 Å
ligand 0TD, 2MG, 4OC, 5MC, 7MG, M2G, MA6, MG, PSU, UR3, ZN enzyme
Gene
Ontology
ChainFunctionProcessComponent
B


C


D


E


F


G


H


I


J


K


L


M


N


O


P


Q


R


S


T


U


Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (2319 Kb) [Save to disk]
  • Biological Unit Coordinates (4dv4.pdb1.gz) 2271 Kb
  • LPC: Ligand-Protein Contacts for 4DV4
  • CSU: Contacts of Structural Units for 4DV4
  • Structure Factors (3208 Kb)
  • Retrieve 4DV4 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4DV4 from S2C, [Save to disk]
  • Re-refined 4dv4 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4DV4 in 3D
  • Proteopedia, because life has more than 2D.
  • On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure.
  • On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.
  • Visual 3D analysis of 4DV4
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 4DV4, from MSDmotif at EBI
  • Fold representative 4dv4 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4dv4_B] [4dv4_N] [4dv4_D] [4dv4_Q] [4dv4_R] [4dv4_J] [4dv4_A] [4dv4_U] [4dv4_S] [4dv4_M] [4dv4_K] [4dv4] [4dv4_T] [4dv4_O] [4dv4_G] [4dv4_I] [4dv4_P] [4dv4_C] [4dv4_L] [4dv4_F] [4dv4_E] [4dv4_H]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 4DV4: [KH] [Ribosomal_S10] [Ribosomal_S15] [Ribosomal_S4] [S4 ] by SMART
  • Other resources with information on 4DV4
  • Community annotation for 4DV4 at PDBWiki (http://pdbwiki.org)

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