3G96 Rna Binding Protein Rna date Feb 12, 2009
title Crystal Structure Of The Bacillus Anthracis Glms Ribozyme Bo Man6p
authors S.A.Strobel, J.C.Cochrane, S.V.Lipchock, K.D.Smith
compound source
Molecule: U1 Small Nuclear Ribonucleoprotein A
Chain: A, B, C, D
Fragment: Rna Binding Domain (Unp Residues 1 To 98)
Engineered: Yes
Mutation: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Snrpa
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet11

Molecule: Rna (5'-R(Ap(A2m)Pgpcpgpcpcpapgpapapc
Chain: E, F, G, H
Engineered: Yes

Synthetic: Yes
Other_details: Chemically Synthesized

Molecule: Glms Ribozyme
Chain: P, Q, R, S
Engineered: Yes

Synthetic: Yes
Other_details: In Vitro Transcribed From A Dna Template
symmetry Space Group: P 1 21 1
R_factor 0.255 R_Free 0.311
crystal
cell
length a length b length c angle alpha angle beta angle gamma
47.401 232.369 104.657 90.00 90.65 90.00
method X-Ray Diffractionresolution 3.01 Å
ligand 6MN, A2M, GTP, MG enzyme
Primary referenceStructural and chemical basis for glucosamine 6-phosphate binding and activation of the glmS ribozyme., Cochrane JC, Lipchock SV, Smith KD, Strobel SA, Biochemistry. 2009 Apr 21;48(15):3239-46. PMID:19228039
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (322 Kb) [Save to disk]
  • Biological Unit Coordinates (3g96.pdb1.gz) 197 Kb
  • Biological Unit Coordinates (3g96.pdb2.gz) 100 Kb
  • Biological Unit Coordinates (3g96.pdb3.gz) 144 Kb
  • Biological Unit Coordinates (3g96.pdb4.gz) 108 Kb
  • LPC: Ligand-Protein Contacts for 3G96
  • CSU: Contacts of Structural Units for 3G96
  • Structure Factors (647 Kb)
  • Retrieve 3G96 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3G96 from S2C, [Save to disk]
  • Re-refined 3g96 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3G96 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 3G96
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Electron Density related parameters from EDS Electron Density Server, at Upsala
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 3G96, from MSDmotif at EBI
  • Fold representative 3g96 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3g96_D] [3g96_P] [3g96_A] [3g96] [3g96_C] [3g96_Q] [3g96_F] [3g96_G] [3g96_S] [3g96_E] [3g96_R] [3g96_H] [3g96_B]
  • SWISS-PROT database: [P09012]
  • Domain organization of [SNRPA_HUMAN] by SWISSPFAM
  • Domain found in 3G96: [RRM ] by SMART
  • Alignments of the sequence of 3G96 with the sequences similar proteins can be viewed for 3G96's classification [SNRPA_HUMAN] at ProtoMap. Click on "Neighbors List", then on the "See Alignments" button below the list.
  • A sequence distance tree ("phylogenetic tree") can be viewed for 1ACL's classification [SNRPA_HUMAN] at ProtoMap. Click on the Cluster number.
  • Other resources with information on 3G96
  • Community annotation for 3G96 at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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