BIOMD0000000384
type: SBMLModel
creator:
  ORG:
    orgname: Max-Planck-Institute of Molecular Plant Physiology
  n:
    given: Anne
    family: Arnold
species: metaid_0000028
parameter: metaid_0000020
name: Carboxylation
creator:
  ORG:
    orgname: Institute of Biochemistry and Biology, University of Potsdam, 14476 Potsdam, Germany
  n:
    given: Zoran
    family: Nikoloski
rule: metaid_0000031
parameter: metaid_0000008
parameter: metaid_0000010
parameter: metaid_0000009
volume units: 498095
time units: 949038
parameter: metaid_0000017
created:
  W3 CDTF: Wed Oct 19 15:50:44 BST 2011
rule: metaid_0000034
function def: metaid_0000004
rule: metaid_0000029
curated: true
parameter: metaid_0000012
reaction: metaid_0000037
species: metaid_0000026
reaction: metaid_0000038
name: Oxygenation
encodes: GO:0019253
name: PGA consumption
substance units: metaid_0000007
creator:
  ORG:
    orgname: EMBL-EBI
  n:
    given: Vijayalakshmi
    family: Chelliah
modified:
  W3 CDTF: Fri Apr 20 20:53:00 BST 2012
length unit: length
parameter: metaid_0000016
function def: metaid_0000003
name: Arnold2011_Medlyn2002_RuBisCO-CalvinCycle
is: MODEL1109270000
is described by: http://identifiers.org/pubmed/22001849
rule: metaid_0000032
species: metaid_0000024
reaction: metaid_0000036
function def: metaid_0000006
parameter: metaid_0000019
species: metaid_0000023
notes: This model is from the article: A quantitative comparison of Calvin–Benson cycle models Anne Arnold, Zoran Nikoloski Trends in Plant Science 2011 Oct 14. 22001849 , Abstract: The Calvin-Benson cycle (CBC) provides the precursors for biomass synthesis necessary for plant growth. The dynamic behavior and yield of the CBC depend on the environmental conditions and regulation of the cellular state. Accurate quantitative models hold the promise of identifying the key determinants of the tightly regulated CBC function and their effects on the responses in future climates. We provide an integrative analysis of the largest compendium of existing models for photosynthetic processes. Based on the proposed ranking, our framework facilitates the discovery of best-performing models with regard to metabolomics data and of candidates for metabolic engineering. Note: Model of the Calvin cycle with focus on the RuBisCO reaction by Medlyn et al. (2002, DOI:10.1046/j.1365-3040.2002.00891.x ). The parameter values are widely taken from Farquhar et al. (1980,DOI:10.1007/BF00386231 ). The initial metabolite values are chosen from the data set of Zhu et al. (2007,DOI:10.1104/pp.107.103713) . A detailed description of all modifications is given in the model described by Arnold and Nikoloski (2011,PMID:22001849 .
parameter: metaid_0000015
species: metaid_0000027
units def: metaid_0000007
area units: 498119
occurs in: http://identifiers.org/taxonomy/33090
rule: metaid_0000030
reaction: metaid_0000035
parameter: metaid_0000021
parameter: metaid_0000011
function def: metaid_0000005
name: NADPH production
rule: metaid_0000033
compartment: metaid_0000022
parameter: metaid_0000018
parameter: metaid_0000013
species: metaid_0000025
parameter: metaid_0000014

metaid_0000028
type: Species
is version of: CHEBI:25523
constant: false
boundary condition: true
has only substance units: false
initial concentration: 0.29
initial amount: NaN
in compartment: metaid_0000022
name: NADP

metaid_0000022
type: Compartment
constant: true
size: 1.0
spatial dimensions: 3.0
name: chloroplast

metaid_0000020
type: Parameter
is: SBO:0000009
constant: false
value: 0.263964911408408
name: phi

metaid_0000008
type: Parameter
constant: true
value: 3.2
name: Rp

metaid_0000010
type: Parameter
notes: (p. 1170)
is: SBO:0000009
constant: true
value: 0.3
name: alpha

metaid_0000009
type: Parameter
is: SBO:0000009
constant: true
value: 0.5
name: Nt

metaid_0000017
type: Parameter
notes: Bernacchi et al. (2001) Equation (8), Table 1
is: SBO:0000009
constant: true
value: 406.066146391504
name: Kc

metaid_0000012
type: Parameter
notes: assumed J = 0.9 Jmax (p. 1172); converted into [mM] using Winter et al. (1994) subcellular stroma volume, BioNumbers (ID: 105594)
is: SBO:0000009
constant: false
value: 4.8582995951417
name: J

metaid_0000037
type: Reaction
kinetic law: 995624
modifier: 995612
product: 995600
reactant: 995588
fast: false
reversible: false
name: PGA consumption

metaid_0000025
type: Species
is version of: CHEBI:16474
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.21
initial amount: NaN
in compartment: metaid_0000022
name: NADPH

995600
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000023

metaid_0000023
type: Species
is version of: CHEBI:16710
constant: true
boundary condition: true
has only substance units: false
initial concentration: 2.0
initial amount: NaN
in compartment: metaid_0000022
name: RuBP

995588
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000024

metaid_0000024
type: Species
is version of: CHEBI:17050
constant: false
boundary condition: false
has only substance units: false
initial concentration: 2.4
initial amount: NaN
in compartment: metaid_0000022
name: PGA

metaid_0000026
type: Species
boundary condition: true
in compartment: metaid_0000022
is version of: CHEBI:16526
constant: true
notes: 0.7* 350 [µbar] (p. 1172)
name: CO2
initial concentration: 245.0
initial amount: NaN
has only substance units: false

metaid_0000038
type: Reaction
kinetic law: 995660
product: 995648
reactant: 995636
fast: false
reversible: false
name: NADPH production

995648
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000025

995636
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000028

995454
type: SBMLUnit
exponent: 1.0
scale: -3
multipler: 1.0
kind: MOLE

metaid_0000016
type: Parameter
constant: false
value: 0.531787796640465
name: Vomax

metaid_0000036
type: Reaction
kinetic law: 995576
product: 995564
reactant: 995551
reactant: 995538
reactant: 995526
fast: false
reversible: false
name: PGA production - v_o

995564
type: SpeciesReference
stoichiometry: 1.5
species: metaid_0000024

995551
type: SpeciesReference
stoichiometry: 2.0
species: metaid_0000025

995538
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000027

metaid_0000027
type: Species
in compartment: metaid_0000022
initial concentration: 210.0
constant: true
has only substance units: false
boundary condition: true
notes: [mbar]
initial amount: NaN
is version of: CHEBI:15379
name: O2

995526
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000023

metaid_0000019
type: Parameter
is: SBO:0000009
constant: false
value: 0.899589030506691
name: Vj

metaid_0000015
type: Parameter
notes: average of corresponding values of Table 2; converted into [mM] using Winter et al. (1994) subcellular stroma volume, BioNumbers (ID: 105594)
is: SBO:0000009
constant: true
value: 2.53232284114507
name: Vcmax

metaid_0000035
type: Reaction
kinetic law: 995514
product: 995502
reactant: 995490
reactant: 995478
reactant: 995466
fast: false
reversible: false
name: PGA production - v_c

995502
type: SpeciesReference
stoichiometry: 2.0
species: metaid_0000024

995490
type: SpeciesReference
stoichiometry: 2.0
species: metaid_0000025

995478
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000026

995466
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000023

metaid_0000021
type: Parameter
is: SBO:0000009
constant: false
value: 0.646926785453086
name: Vc

metaid_0000011
type: Parameter
is: SBO:0000009
constant: true
value: 1000.0
name: Q

metaid_0000018
type: Parameter
notes: Bernacchi et al. (2001) Equation (8), Table 1
constant: true
value: 276.900084789612
name: Ko

metaid_0000013
type: Parameter
notes: Bernacchi et al. (2001) Equation (8), Table 1
is: SBO:0000009
constant: true
value: 42.8926627111176
name: Gamma

metaid_0000014
type: Parameter
notes: (p. 1170)
is: SBO:0000009
constant: true
value: 0.9
name: teta