3RUB

CRYSTAL STRUCTURE OF THE UNACTIVATED FORM OF RIBULOSE-1,5-BISPHOSPHATE CARBOXYLASE(SLASH)OXYGENASE FROM TOBACCO REFINED AT 2.0-ANGSTROMS RESOLUTION


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal structure of the unactivated form of ribulose-1,5-bisphosphate carboxylase/oxygenase from tobacco refined at 2.0-A resolution.

Curmi, P.M.Cascio, D.Sweet, R.M.Eisenberg, D.Schreuder, H.

(1992) J.Biol.Chem. 267: 16980-16989


  • PubMed Abstract: 
  • The structure of the unactivated form of ribulose-1,5-bisphosphate carboxylase/oxygenase was refined at a resolution of 2.0 A to an R-factor of 17.1%. The previous model (Chapman et al., 1988) was extensively rebuilt, and the small subunit was retrac ...

    The structure of the unactivated form of ribulose-1,5-bisphosphate carboxylase/oxygenase was refined at a resolution of 2.0 A to an R-factor of 17.1%. The previous model (Chapman et al., 1988) was extensively rebuilt, and the small subunit was retraced. The refined model consists of residues 22-63 and 69-467 of the large subunit and the complete small subunit. A striking feature of the model is that several loops have very high B-factors, probably representing mobile regions of the molecule. An examination of the intersubunit contacts shows that the L8S8 hexadecamer is composed of four L2 dimers. The dominant contacts between these L2 dimers are formed by the small subunits. This suggests that the small subunits may be essential for maintaining the integrity of the L8S8 structure. The active site shows differences between the unactivated form and the quaternary complex. In particular, Lys334 has moved out of the active site by about 10A. This residue lies on loop 6 of the alpha beta barrel, which is a particularly mobile loop. The site of ribulose-1,5-bisphosphate carboxylase/oxygenase activation is well ordered in the absence of the carbamylation of Lys201 and Mg2+ binding. The residues are held poised by a network of hydrogen bonds. In the unactivated state, the active site is accessible to substrate binding.


    Related Citations: 
    • Sliding-Layer Conformational Change Limited by the Quaternary Structure of Plant Rubis/Co
      Chapman, M.S.,Suh, S.W.,Cascio, D.,Smith, W.W.,Eisenberg, D.
      (1987) Nature 329: 354
    • Tertiary Structure of Plant Rubis/Co: Domains and Their Contacts
      Chapman, M.S.,Suh, S.W.,Curmi, P.M.G.,Cascio, D.,Smith, W.W.,Eisenberg, D.S.
      (1988) Science 241: 71
    • Crystal Structure of the Inactive Form of Ribulose-1,5-Bisphosphate Carboxylase(Slash)Oxygenase (Rubis/Co): Disulfide Bonds and Active Site Region
      Schreuder, H.,Curmi, P.M.G.,Cascio, D.,Eisenberg, D.
      () TO BE PUBLISHED --: --


    Organizational Affiliation

    Department of Chemistry and Biochemistry, University of California, Los Angeles 90024.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
RIBULOSE 1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE, FORM III
L
477Nicotiana tabacumGene Names: rbcL (rbcA)
EC: 4.1.1.39
Find proteins for P00876 (Nicotiana tabacum)
Go to UniProtKB:  P00876
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
RIBULOSE 1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE, FORM III
S
123Nicotiana tabacumGene Names: RBCS
EC: 4.1.1.39
Find proteins for P69249 (Nicotiana tabacum)
Go to UniProtKB:  P69249
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
L
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
ASN
Query on ASN

Download SDF File 
Download CCD File 
L
ASPARAGINE
C4 H8 N2 O3
DCXYFEDJOCDNAF-REOHCLBHSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • Space Group: I 4 2 2
Unit Cell:
Length (Å)Angle (°)
a = 148.700α = 90.00
b = 148.700β = 90.00
c = 137.500γ = 90.00
Software Package:
Software NamePurpose
PROFFTrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1992-10-15
    Type: Initial release
  • Version 1.1: 2008-03-03
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance