3HKZ Transferase date May 26, 2009
title The X-Ray Crystal Structure Of Rna Polymerase From Archaea
authors K.S.Murakami
compound source
Molecule: Dna-Directed Rna Polymerase Subunit A'
Chain: A, I
Ec: 2.7.7.6
 Organism_scientific: Sulfolobus Solfataricus
Organism_taxid: 273057
Strain: P2

Molecule: Dna-Directed Rna Polymerase Subunit A''
Chain: C, M
Ec: 2.7.7.6
Organism_scientific: Sulfolobus Solfataricus
Organism_taxid: 273057
Strain: P2

Molecule: Dna-Directed Rna Polymerase Subunit B
Chain: B, J
Organism_scientific: Sulfolobus Solfataricus
Organism_taxid: 273057
Strain: P2

Molecule: Dna-Directed Rna Polymerase Subunit D
Chain: D, O
Ec: 2.7.7.6
Organism_scientific: Sulfolobus Solfataricus
Organism_taxid: 273057
Strain: P2

Molecule: Dna-Directed Rna Polymerase, Subunit E' (Rpoe1)
Chain: E, Q
Ec: 2.7.7.6
Organism_scientific: Sulfolobus Solfataricus
Organism_taxid: 273057
Strain: P2

Molecule: Dna-Directed Rna Polymerase, Subunit F (Rpof)
Chain: F, R
Synonym: Putative Uncharacterized Protein Orf-C20_042
Ec: 2.7.7.6
Organism_scientific: Sulfolobus Solfataricus
Organism_taxid: 273057
Strain: P2

Molecule: Dna-Directed Rna Polymerase, Subunit G (Rpog)
Chain: G, S
Ec: 2.7.7.6
Organism_scientific: Sulfolobus Solfataricus
Organism_taxid: 273057
Strain: P2

Molecule: Dna-Directed Rna Polymerase Subunit H
Chain: H, T
Ec: 2.7.7.6
Organism_scientific: Sulfolobus Solfataricus
Organism_taxid: 273057
Strain: P2

Molecule: Dna-Directed Rna Polymerase Subunit K
Chain: K, U
Ec: 2.7.7.6
Organism_scientific: Sulfolobus Solfataricus
Organism_taxid: 273057
Strain: P2

Molecule: Dna-Directed Rna Polymerase Subunit L
Chain: L, V
Ec: 2.7.7.6
Organism_scientific: Sulfolobus Solfataricus
Organism_taxid: 273057
Strain: P2

Molecule: Dna-Directed Rna Polymerase Subunit N
Chain: N, W
Ec: 2.7.7.6
Organism_scientific: Sulfolobus Solfataricus
Organism_taxid: 273057
Strain: P2

Molecule: Dna-Directed Rna Polymerase Subunit P
Chain: P, X
Ec: 2.7.7.6
Organism_scientific: Sulfolobus Solfataricus
Organism_taxid: 273057
Strain: P2

Molecule: Dna-Directed Rna Polymerase Subunit 13
Chain: Y, Z
Organism_scientific: Sulfolobus Solfataricus
Organism_taxid: 273057
Strain: P2
symmetry Space Group: P 1 21 1
R_factor 0.265 R_Free 0.341
crystal
cell
length a length b length c angle alpha angle beta angle gamma
125.820 201.235 196.050 90.00 100.92 90.00
method X-Ray Diffractionresolution 3.40 Å
ligand F3S, MG, ZN enzyme Transferase E.C.2.7.7.6 BRENDA
note 3HKZ is a representative structure
Gene
Ontology
ChainFunctionProcessComponent
A, I


E, Q


F, R


J, B


K, U


M, C


N, W


O, D


S, G
  • DNA-directed 5'-3' RNA polym...


    • T, H


    V, L


    X, P


    Primary referenceThe X-ray crystal structure of RNA polymerase from Archaea., Hirata A, Klein BJ, Murakami KS, Nature. 2008 Feb 14;451(7180):851-4. Epub 2008 Jan 30. PMID:18235446
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (1057 Kb) [Save to disk]
  • Biological Unit Coordinates (3hkz.pdb1.gz) 532 Kb
  • Biological Unit Coordinates (3hkz.pdb2.gz) 530 Kb
  • LPC: Ligand-Protein Contacts for 3HKZ
  • CSU: Contacts of Structural Units for 3HKZ
  • Likely Quarternary Molecular Structure file(s) for 3HKZ
  • Structure Factors (1988 Kb)
  • Retrieve 3HKZ in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3HKZ from S2C, [Save to disk]
  • Re-refined 3hkz structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 3HKZ 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 3HKZ
  • 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
  • 3D motif for 3HKZ, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3hkz_U] [3hkz_C] [3hkz_I] [3hkz_S] [3hkz_W] [3hkz_Z] [3hkz_Y] [3hkz_D] [3hkz_P] [3hkz_L] [3hkz_O] [3hkz_H] [3hkz_T] [3hkz_K] [3hkz_G] [3hkz_Q] [3hkz_J] [3hkz_B] [3hkz_A] [3hkz_F] [3hkz_R] [3hkz_X] [3hkz_E] [3hkz_M] [3hkz] [3hkz_V] [3hkz_N]
  • SWISS-PROT database: [Q980A3] [Q980B8] [Q980L5] [Q980R1] [Q9UXD9] [Q980R2] [P58192] [P95989] [Q980Q9] [Q97ZJ9] [Q980K0] [Q980Z8] [Q97ZX7]
  • Domain organization of [Q980A3_SULSO] [Q980B8_SULSO] [Q980L5_SULSO] [Q980R1_SULSO] [Q9UXD9_SULSO] [RPOA1_SULSO] [RPOA2_SULSO] [RPOD_SULSO] [RPOH_SULSO] [RPOK_SULSO] [RPOL_SULSO] [RPON_SULSO] [RPOP_SULSO] by SWISSPFAM
  • Domains found in 3HKZ: [RNA_pol_Rpb6] [RPOLA_N] [RPOLCX] [RPOLD] [S1 ] by SMART
    • Other resources with information on 3HKZ
  • Community annotation for 3HKZ 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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