1U8R Metal-Binding Protein,Transcription Dna date Aug 06, 2004
title Crystal Structure Of An Ider-Dna Complex Reveals A Conformat Change In Activated Ider For Base-Specific Interactions
authors G.Wisedchaisri, R.K.Holmes, W.G.J.Hol
compound source
Molecule: Mbta Operator Dna
Chain: E, K
Engineered: Yes
Synthetic: Yes

Molecule: Mbtb Operator Dna
Chain: F, L
Engineered: Yes

Synthetic: Yes

Molecule: Iron-Dependent Repressor Ider
Chain: A, B, C, D, G, H, I, J
Engineered: Yes

Organism_scientific: Mycobacterium Tuberculosis
Organism_taxid: 1773
Gene: Ider, Dtxr
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Dh5alpha
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pbluescript II Ks (+--)
symmetry Space Group: P 31
R_factor 0.230 R_Free 0.265
crystal
cell
length a length b length c angle alpha angle beta angle gamma
107.959 107.959 215.124 90.00 90.00 120.00
method X-Ray Diffractionresolution 2.75 Å
ligand CO, NA enzyme
related structures by homologous chain: 1B1B, 1G3Y
Gene
Ontology
ChainFunctionProcessComponent
H, A, J, D, C, I, G, B


Primary referenceCrystal structure of an IdeR-DNA complex reveals a conformational change in activated IdeR for base-specific interactions., Wisedchaisri G, Holmes RK, Hol WG, J Mol Biol 2004 Sep 24;342(4):1155-69. PMID:15351642
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (337 Kb) [Save to disk]
  • Biological Unit Coordinates (1u8r.pdb1.gz) 167 Kb
  • Biological Unit Coordinates (1u8r.pdb2.gz) 167 Kb
  • LPC: Ligand-Protein Contacts for 1U8R
  • CSU: Contacts of Structural Units for 1U8R
  • Likely Quarternary Molecular Structure file(s) for 1U8R
  • Structure Factors (535 Kb)
  • Retrieve 1U8R in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1U8R from S2C, [Save to disk]
  • Re-refined 1u8r structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1U8R 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 1U8R
  • 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 1U8R, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1u8ra1, region A:1-64 [Jmol] [rasmolscript] [script source]
        - Domain d1u8ra3, region A:151-230 [Jmol] [rasmolscript] [script source]
        - Domain d1u8ra2, region A:65-141 [Jmol] [rasmolscript] [script source]
        - Domain d1u8rb1, region B:1-64 [Jmol] [rasmolscript] [script source]
        - Domain d1u8rb3, region B:151-230 [Jmol] [rasmolscript] [script source]
        - Domain d1u8rb2, region B:65-141 [Jmol] [rasmolscript] [script source]
        - Domain d1u8rc1, region C:1-64 [Jmol] [rasmolscript] [script source]
        - Domain d1u8rc3, region C:151-230 [Jmol] [rasmolscript] [script source]
        - Domain d1u8rc2, region C:65-141 [Jmol] [rasmolscript] [script source]
        - Domain d1u8rd1, region D:1-64 [Jmol] [rasmolscript] [script source]
        - Domain d1u8rd3, region D:151-230 [Jmol] [rasmolscript] [script source]
        - Domain d1u8rd2, region D:65-141 [Jmol] [rasmolscript] [script source]
        - Domain d1u8rg1, region G:1-64 [Jmol] [rasmolscript] [script source]
        - Domain d1u8rg3, region G:151-230 [Jmol] [rasmolscript] [script source]
        - Domain d1u8rg2, region G:65-141 [Jmol] [rasmolscript] [script source]
        - Domain d1u8rh1, region H:1-64 [Jmol] [rasmolscript] [script source]
        - Domain d1u8rh3, region H:150-230 [Jmol] [rasmolscript] [script source]
        - Domain d1u8rh2, region H:65-141 [Jmol] [rasmolscript] [script source]
        - Domain d1u8ri1, region I:1-64 [Jmol] [rasmolscript] [script source]
        - Domain d1u8ri3, region I:151-230 [Jmol] [rasmolscript] [script source]
        - Domain d1u8ri2, region I:65-141 [Jmol] [rasmolscript] [script source]
        - Domain d1u8rj1, region J:1-64 [Jmol] [rasmolscript] [script source]
        - Domain d1u8rj3, region J:150-230 [Jmol] [rasmolscript] [script source]
        - Domain d1u8rj2, region J:65-141 [Jmol] [rasmolscript] [script source]
  • Class (fold), Architecture (subfold), Topology, Homologous superfamily from CATH
  • Summaries and structural analyses of PDB data files from PDBSum
  • Identification of Protein Pockets & Cavities at CASTp
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1u8r_F] [1u8r_C] [1u8r_J] [1u8r_G] [1u8r_E] [1u8r_D] [1u8r_I] [1u8r_A] [1u8r_B] [1u8r] [1u8r_H] [1u8r_L] [1u8r_K]
  • SWISS-PROT database: [P0A672]
  • Domain organization of [IDER_MYCTU] by SWISSPFAM
  • Domains found in 1U8R: [FeoA] [HTH_DTXR ] by SMART
  • Other resources with information on 1U8R
  • Community annotation for 1U8R 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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