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PDBsum entry 1rbl

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protein ligands metals Protein-protein interface(s) links
Lyase PDB id
1rbl
Jmol
Contents
Protein chains
(+ 2 more) 467 a.a. *
(+ 2 more) 109 a.a. *
Ligands
CAP ×8
FMT ×8
Metals
_MG ×8
Waters ×292
* Residue conservation analysis
PDB id:
1rbl
Name: Lyase
Title: Structure determination and refinement of ribulose 1,5 bisph carboxylase(slash)oxygenase from synechococcus pcc6301
Structure: Ribulose 1,5 bisphosphate carboxylase/oxygenase ( chain). Chain: a, b, c, d, e, f, g, h. Engineered: yes. Ribulose 1,5 bisphosphate carboxylase/oxygenase ( chain). Chain: m, i, n, j, o, k, p, l. Engineered: yes
Source: Synechococcus elongatus. Organism_taxid: 269084. Strain: pcc 6301. Strain: pcc 6301
Biol. unit: 60mer (from PQS)
Resolution:
2.20Å     R-factor:   0.200    
Authors: J.Newman,S.Gutteridge,C.-I.Branden,T.A.Jones
Key ref:
J.Newman et al. (1993). Structure determination and refinement of ribulose 1,5-bisphosphate carboxylase/oxygenase from Synechococcus PCC6301. Acta Crystallogr D Biol Crystallogr, 49, 548-560. PubMed id: 15299492 DOI: 10.1107/S090744499300530X
Date:
12-May-93     Release date:   22-Jun-94    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P00880  (RBL_SYNP6) -  Ribulose bisphosphate carboxylase large chain
Seq:
Struc:
472 a.a.
467 a.a.*
Protein chains
Pfam   ArchSchema ?
P04716  (RBS_SYNP6) -  Ribulose bisphosphate carboxylase small chain
Seq:
Struc:
111 a.a.
109 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 6 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: Chains A, M, B, I, C, N, D, J, E, O, F, K, G, P, H, L: E.C.4.1.1.39  - Ribulose-bisphosphate carboxylase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: 2 3-phospho-D-glycerate + 2 H+ = D-ribulose 1,5-bisphosphate + CO2 + H2O
2 × 3-phospho-D-glycerate
+ 2 × H(+)
=
D-ribulose 1,5-bisphosphate
Bound ligand (Het Group name = CAP)
matches with 85.71% similarity
+
CO(2)
Bound ligand (Het Group name = FMT)
corresponds exactly
+ H(2)O
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     oxidation-reduction process   5 terms 
  Biochemical function     oxidoreductase activity     6 terms  

 

 
    reference    
 
 
DOI no: 10.1107/S090744499300530X Acta Crystallogr D Biol Crystallogr 49:548-560 (1993)
PubMed id: 15299492  
 
 
Structure determination and refinement of ribulose 1,5-bisphosphate carboxylase/oxygenase from Synechococcus PCC6301.
J.Newman, C.I.Branden, T.A.Jones.
 
  ABSTRACT  
 
The structure of an activated quaternary complex of ribulose 1,5-bisphosphate carboxylase/oxygenase (rubisco) from Synechococcus PCC6301 has been solved by molecular replacement. The protein crystallizes in an orthorhombic P2(1)2(1)2(1) unit cell with a complete L(8)S(8) complex consisting of 4608 residues (37 680 non-hydrogen atoms) in the asymmetric unit. Data were collected both on film and image plate using synchrotron radiation; there were 218 276 unique reflections in the final 2.2 A data set. The eightfold non-crystallographic symmetry could be used both to improve map quality and to reduce the computing requirements of refinement. The coordinates were refined using strict non-crystallographic symmetry constraints. The stereochemistry of the final model is good, and the model has an R value of 20.0% for the reflections between 7 and 2.2 A.
 
  Selected figure(s)  
 
Figure 9.
Fig. 9. A ribbon diagram of an/,2 dimer. The barrel of one L subunit is coloured blue, and the N-terminal domain of the same subunit, cyan. The barrel domain of the second L subunit is red, and its N-terminal domain is magenta. The yellow spheres are Mg 2 ions, and show the positions of the active sites. Both this figure and the previous figure were generated in O.
Figure 15.
Fig. 15. Pepflip values versus residue number. The dashed line shows the 2.5 threshold suggested by Jones et al. Table 3 summarizes the residues which have~ a pepflip >__ 2.5.
 
  The above figures are reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (1993, 49, 548-560) copyright 1993.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21765418 A.Bracher, A.Starling-Windhof, F.U.Hartl, and M.Hayer-Hartl (2011).
Crystal structure of a chaperone-bound assembly intermediate of form I Rubisco.
  Nat Struct Mol Biol, 18, 875-880.
PDB code: 3rg6
20075914 C.Liu, A.L.Young, A.Starling-Windhof, A.Bracher, S.Saschenbrecker, B.V.Rao, K.V.Rao, O.Berninghausen, T.Mielke, F.U.Hartl, R.Beckmann, and M.Hayer-Hartl (2010).
Coupled chaperone action in folding and assembly of hexadecameric Rubisco.
  Nature, 463, 197-202.
PDB codes: 2wvw 3hyb
19705820 S.Satagopan, S.S.Scott, T.G.Smith, and F.R.Tabita (2009).
A Rubisco mutant that confers growth under a normally "inhibitory" oxygen concentration.
  Biochemistry, 48, 9076-9083.  
18487131 F.R.Tabita, T.E.Hanson, S.Satagopan, B.H.Witte, and N.E.Kreel (2008).
Phylogenetic and evolutionary relationships of RubisCO and the RubisCO-like proteins and the functional lessons provided by diverse molecular forms.
  Philos Trans R Soc Lond B Biol Sci, 363, 2629-2640.  
11435112 K.Kitano, N.Maeda, T.Fukui, H.Atomi, T.Imanaka, and K.Miki (2001).
Crystal structure of a novel-type archaeal rubisco with pentagonal symmetry.
  Structure, 9, 473-481.
PDB code: 1geh
  11641402 T.C.Taylor, A.Backlund, K.Bjorhall, R.J.Spreitzer, and I.Andersson (2001).
First crystal structure of Rubisco from a green alga, Chlamydomonas reinhardtii.
  J Biol Chem, 276, 48159-48164.
PDB code: 1gk8
8900108 N.Shibata, T.Inoue, K.Fukuhara, Y.Nagara, R.Kitagawa, S.Harada, N.Kasai, K.Uemura, K.Kato, A.Yokota, and Y.Kai (1996).
Orderly disposition of heterogeneous small subunits in D-ribulose-1,5-bisphosphate carboxylase/oxygenase from spinach.
  J Biol Chem, 271, 26449-26452.
PDB code: 1bur
7922027 J.Newman, and S.Gutteridge (1994).
Structure of an effector-induced inactivated state of ribulose 1,5-bisphosphate carboxylase/oxygenase: the binary complex between enzyme and xylulose 1,5-bisphosphate.
  Structure, 2, 495-502.
PDB code: 1rsc
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.