4YG2 Transferase Transcription date Feb 25, 2015
title X-Ray Crystal Structur Of Escherichia Coli Rna Polymerase Si Holoenzyme
authors K.S.Murakami
compound source
Molecule: Dna-Directed Rna Polymerase Subunit Alpha
Chain: A, B, G, H
Synonym: Rnap Subunit Alpha,Rna Polymerase Subunit Alpha, Transcriptase Subunit Alpha;
Ec: 2.7.7.6
Engineered: Yes
Organism_scientific: Escherichia Coli O157:H7
Organism_taxid: 83334
Strain: O157:H7
Gene: Rpoa, Z4665, Ecs4160
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pgemabc

Molecule: Dna-Directed Rna Polymerase Subunit Beta
Chain: C, I
Synonym: Rnap Subunit Beta,Rna Polymerase Subunit Beta,Tran Subunit Beta;
Ec: 2.7.7.6
Engineered: Yes

Organism_scientific: Escherichia Coli O157:H7
Organism_taxid: 83334
Strain: O157:H7
Gene: Rpob, Z5560, Ecs4910
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pgemabc

Molecule: Dna-Directed Rna Polymerase Subunit Beta'
Chain: D, J
Synonym: Rnap Subunit Beta',Rna Polymerase Subunit Beta', Transcriptase Subunit Beta';
Ec: 2.7.7.6
Engineered: Yes

Organism_scientific: Escherichia Coli O157:H7
Organism_taxid: 83334
Strain: O157:H7
Gene: Rpoc, Z5561, Ecs4911
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pgemabc

Molecule: Dna-Directed Rna Polymerase Subunit Omega
Chain: E, K
Synonym: Rnap Omega Subunit,Rna Polymerase Omega Subunit, Transcriptase Subunit Omega;
Ec: 2.7.7.6
Engineered: Yes

Organism_scientific: Escherichia Coli O157:H7
Organism_taxid: 83334
Strain: O157:H7
Gene: Rpoz, Z5075, Ecs4524
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pacycduet-1_ec_rpoz

Molecule: Rna Polymerase Sigma Factor Rpod
Chain: F, L
Synonym: Sigma-70
Engineered: Yes

Organism_scientific: Escherichia Coli K12
Organism_taxid: 83333
Strain: K12
Gene: Rpod, Alt, B3067, Jw3039
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pgemd
symmetry Space Group: P 21 21 21
R_factor 0.191 R_Free 0.260
crystal
cell
length a length b length c angle alpha angle beta angle gamma
187.308 205.901 309.185 90.00 90.00 90.00
method X-Ray Diffractionresolution 3.70 Å
ligand MG, ZN enzyme Transferase E.C.2.7.7.6 BRENDA
note 4YG2 supersedes 4IGC
Gene
Ontology
ChainFunctionProcessComponent
A, B, H, G


C, I


F, L


J, D


K, E


Primary referenceX-ray crystal structure of Escherichia coli RNA polymerase sigma70 holoenzyme., Murakami KS, J Biol Chem. 2013 Mar 29;288(13):9126-34. doi: 10.1074/jbc.M112.430900. Epub 2013, Feb 6. PMID:23389035
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (2438 Kb) [Save to disk]
  • Biological Unit Coordinates (4yg2.pdb1.gz) 1234 Kb
  • Biological Unit Coordinates (4yg2.pdb2.gz) 1202 Kb
  • LPC: Ligand-Protein Contacts for 4YG2
  • CSU: Contacts of Structural Units for 4YG2
  • Structure Factors (1917 Kb)
  • Retrieve 4YG2 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4YG2 from S2C, [Save to disk]
  • Re-refined 4yg2 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4YG2 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 4YG2
  • 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 4YG2, from MSDmotif at EBI
  • Fold representative 4yg2 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4yg2_B] [4yg2_E] [4yg2_C] [4yg2] [4yg2_I] [4yg2_K] [4yg2_G] [4yg2_D] [4yg2_A] [4yg2_F] [4yg2_J] [4yg2_H] [4yg2_L]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 4YG2: [RNA_pol_Rpb6] [RPOLA_N] [RPOLD ] by SMART
  • Other resources with information on 4YG2
  • Community annotation for 4YG2 at PDBWiki (http://pdbwiki.org)

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