5RUB

CRYSTALLOGRAPHIC REFINEMENT AND STRUCTURE OF RIBULOSE-1,5-BISPHOSPHATE CARBOXYLASE FROM RHODOSPIRILLUM RUBRUM AT 1.7 ANGSTROMS RESOLUTION


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Crystallographic refinement and structure of ribulose-1,5-bisphosphate carboxylase from Rhodospirillum rubrum at 1.7 A resolution.

Schneider, G.Lindqvist, Y.Lundqvist, T.

(1990) J.Mol.Biol. 211: 989-1008

  • DOI: 10.1016/0022-2836(90)90088-4

  • PubMed Abstract: 
  • The amino acid sequence of ribulose-1,5-bisphosphate carboxylase/oxygenase from Rhodospirillum rubrum has been fitted to the electron density maps. The resulting protein model has been refined to a nominal resolution of 1.7 A using the constrained-re ...

    The amino acid sequence of ribulose-1,5-bisphosphate carboxylase/oxygenase from Rhodospirillum rubrum has been fitted to the electron density maps. The resulting protein model has been refined to a nominal resolution of 1.7 A using the constrained-restrained least-squares refinement program of Sussman and the restrained least-squares refinement program of Hendrickson & Konnert. The crystallographic refinement, based on 76,452 reflections with F greater than sigma (F) in the resolution range 5.5 to 1.7 A resulted in a crystallographic R-factor of 18.0%. The asymmetric unit contains one dimeric ribulose-1,5-biphosphate carboxylase molecule, consisting of 869 amino acid residues and 736 water molecules. The geometry of the refined model is close to ideal, with root-mean-square deviations of 0.018 A in bond lengths and 2.7 degrees in bond angles. Two loop regions, comprising residues 54 to 63 and 324 to 335, and the last ten amino acid residues at the C terminus are disordered in our crystals. The expected trimodal distribution is obtained for the side-chain chi 1-angles with a marked preference for staggered conformation. The hydrogen-bonding pattern in the N-terminal beta-sheet and the parallel sheet in the beta/alpha-barrel is described. A number of hydrogen bonds and salt bridges are involved in domain-domain and subunit-subunit interactions. The subunit-subunit interface in the dimer covers an area of 2800 A2. Considerable deviations from the local 2-fold symmetry are found at both the N terminus (residues 2 to 5) and the C terminus (residues 422 to 457). Furthermore, loop 8 in the beta/alpha-barrel domain has a different conformation in the two subunits. A number of amino acid side-chains have different conformations in the two subunits. Most of these residues are located at the surface of the protein. An analysis of the individual temperature factors indicates a high mobility of the C-terminal region and for some of the loops at the active site. The positions and B-factors for 736 solvent sites have been refined (average B: 45.9 A2). Most of the solvent molecules are bound as clusters to the protein. The active site of the enzyme, especially the environment of the activator Lys191 in the non-activated enzyme is described. Crystallographic refinement at 1.7 A resolution clearly revealed the presence of a cis-proline at the active site. This residue is part of the highly conserved region Lys166-Pro167-Lys168.


    Related Citations: 
    • Crystal Structure of the Complex of Ribulose-1,5-Bisphosphate Carboxylase and a Transition State Analogue, 2-Carboxy-D-Arabinitol 1,5-Bisphosphate
      Lundqvist, T.,Schneider, G.
      (1989) J.Biol.Chem. 264: 7078
    • Crystal Structure of the Binary Complex of Ribulose-1,5-Bisphosphate Carboxylase and its Product, 3-Phospho-D-Glycerate
      Lundqvist, T.,Schneider, G.
      (1988) J.Biol.Chem. 263: 3643
    • Three-Dimensional Structure of Ribulose-1,5-Bisphosphate Carboxylase(Slash)Oxygenase from Rhodospirillum Rubrum at 2.9 Angstroms Resolution
      Schneider, G.,Lindqvist, Y.,Branden, C.-I.,Lorimer, G.
      (1986) Embo J. 5: 3409
    • Crystal Structure of the Ternary Complex of Ribulose-1,5-Bisphosphate Carboxylase, Mg(II), and Activator Co2 at 2.3-Angstroms Resolution
      Lundqvist, T.,Schneider, G.
      (1991) Biochemistry 30: 904
    • Crystal Structure of the Active Site of Ribulose-Bisphosphate Carboxylase
      Andersson, I.,Knight, S.,Schneider, G.,Lindqvist, Y.,Lundqvist, T.,Branden, C.-I.,Lorimer, G.H.
      (1989) Nature 337: 229


    Organizational Affiliation

    Swedish University of Agricultural Sciences, Uppsala Biomedical Centre, Department of Molecular Biology.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
RUBISCO (RIBULOSE-1,5-BISPHOSPHATE CARBOXYLASE(SLASH)OXYGENASE)
A, B
490Rhodospirillum rubrumGene Names: cbbM (cbbL2, rbpL)
EC: 4.1.1.39
Find proteins for P04718 (Rhodospirillum rubrum)
Go to UniProtKB:  P04718
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 65.500α = 90.00
b = 70.600β = 92.10
c = 104.100γ = 90.00
Software Package:
Software NamePurpose
PROLSQrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1991-10-15
    Type: Initial release
  • Version 1.1: 2008-03-25
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-11-29
    Type: Advisory, Derived calculations, Other