4DV2 Ribosome date Feb 22, 2012
title Crystal Structure Of The Thermus Thermophilus 30s Ribosomal With A 16s Rrna Mutation, C912a
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 0.165 R_Free 0.223
crystal
cell
length a length b length c angle alpha angle beta angle gamma
403.743 403.743 173.221 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] (2325 Kb) [Save to disk]
  • Biological Unit Coordinates (4dv2.pdb1.gz) 2276 Kb
  • LPC: Ligand-Protein Contacts for 4DV2
  • CSU: Contacts of Structural Units for 4DV2
  • Structure Factors (2980 Kb)
  • Retrieve 4DV2 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4DV2 from S2C, [Save to disk]
  • Re-refined 4dv2 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4DV2 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 4DV2
  • 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 4DV2, from MSDmotif at EBI
  • Fold representative 4dv2 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4dv2_A] [4dv2_K] [4dv2_L] [4dv2_J] [4dv2] [4dv2_U] [4dv2_G] [4dv2_T] [4dv2_N] [4dv2_B] [4dv2_M] [4dv2_O] [4dv2_D] [4dv2_H] [4dv2_Q] [4dv2_E] [4dv2_C] [4dv2_I] [4dv2_F] [4dv2_P] [4dv2_S] [4dv2_R]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 4DV2: [KH] [Ribosomal_S10] [Ribosomal_S15] [Ribosomal_S4] [S4 ] by SMART
  • Other resources with information on 4DV2
  • Community annotation for 4DV2 at PDBWiki (http://pdbwiki.org)

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