metaid_0000033
kinetic law: 983709
product: 983697
reactant: 983685
fast: false
reversible: false
name: NADPH production
type: Reaction

983648
stoichiometry: 1.0
species: metaid_0000020
type: SpeciesReference

metaid_0000009
notes: Equation (19)
is: SBO:0000009
constant: true
value: 3.2
name: Rp
type: Parameter

metaid_0000015
notes: Equation (17)
is: SBO:0000009
constant: false
value: 0.267272727272727
name: phi
type: Parameter

983515
stoichiometry: 2.0
species: metaid_0000022
type: SpeciesReference

metaid_0000024
type: Species
has only substance units: false
is version of: CHEBI:15379
initial amount: NaN
name: O2
constant: true
boundary condition: true
in compartment: metaid_0000019
initial concentration: 210.0
notes: [mbar]

metaid_0000022
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_0000019
name: NADPH
type: Species

983685
stoichiometry: 1.0
species: metaid_0000025
type: SpeciesReference

metaid_0000019
constant: true
size: 1.0
spatial dimensions: 3.0
name: chloroplast
type: Compartment

983600
stoichiometry: 1.5
species: metaid_0000021
type: SpeciesReference

metaid_0000032
kinetic law: 983673
modifier: 983661
product: 983648
reactant: 983636
fast: false
reversible: false
name: PGA consumption
type: Reaction

metaid_0000008
notes: converted into [mM] using Winter et al. (1994) subcellular stroma volume
is: SBO:0000009
constant: true
value: 1.33846153846154
name: E
type: Parameter

metaid_0000014
notes: converted into [mM] using Winter et al. (1994) subcellular stroma volume
is: SBO:0000009
constant: false
value: 5.92307692307692
name: j
type: Parameter

metaid_0000025
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_0000019
name: NADP
type: Species

metaid_0000023
notes: [µbar]
constant: true
is version of: CHEBI:16526
type: Species
boundary condition: true
initial amount: NaN
has only substance units: false
initial concentration: 230.0
in compartment: metaid_0000019
name: CO2

983576
stoichiometry: 1.0
species: metaid_0000023
type: SpeciesReference

metaid_0000018
is: SBO:0000009
constant: true
value: 330.0
name: Ko
type: Parameter

metaid_0000031
product: 983600
reactant: 983576
reversible: false
reactant: 983564
modifier: 983612
type: Reaction
kinetic law: 983624
fast: false
name: PGA production - v_o
reactant: 983588

983503
stoichiometry: 1.0
species: metaid_0000023
type: SpeciesReference

983564
stoichiometry: 1.0
species: metaid_0000020
type: SpeciesReference

metaid_0000013
is: SBO:0000009
constant: false
value: 385.0
name: jp
type: Parameter

983491
stoichiometry: 1.0
species: metaid_0000020
type: SpeciesReference

983636
stoichiometry: 1.0
species: metaid_0000021
type: SpeciesReference

metaid_0000020
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_0000019
name: RuBP
type: Species

BIOMD0000000383
encodes: GO:0019253
species: metaid_0000021
length unit: length
species: metaid_0000024
parameter: metaid_0000009
occurs in: http://identifiers.org/taxonomy/33090
rule: metaid_0000026
function def: metaid_0000005
is described by: http://identifiers.org/pubmed/22001849
parameter: metaid_0000014
rule: metaid_0000028
parameter: metaid_0000015
parameter: metaid_0000017
reaction: metaid_0000033
reaction: metaid_0000032
parameter: metaid_0000010
species: metaid_0000022
parameter: metaid_0000011
area units: 498119
created:
  W3 CDTF: Wed Oct 19 15:49:55 BST 2011
parameter: metaid_0000008
rule: metaid_0000027
name: NADPH production
species: metaid_0000025
parameter: metaid_0000012
parameter: metaid_0000013
rule: metaid_0000029
name: PGA consumption - Farquhar
type: SBMLModel
function def: metaid_0000004
substance units: metaid_0000007
compartment: metaid_0000019
function def: metaid_0000006
creator:
  ORG:
    orgname: Institute of Biochemistry and Biology, University of Potsdam, 14476 Potsdam, Germany
  n:
    given: Zoran
    family: Nikoloski
creator:
  ORG:
    orgname: EMBL-EBI
  n:
    given: Vijayalakshmi
    family: Chelliah
curated: true
modified:
  W3 CDTF: Fri Apr 20 20:53:17 BST 2012
name: Arnold2011_Farquhar1980_RuBisCO-CalvinCycle
is: MODEL1109210000
creator:
  ORG:
    orgname: Max-Planck-Institute of Molecular Plant Physiology
  n:
    given: Anne
    family: Arnold
species: metaid_0000020
name: Carboxylation
name: Oxygenation
parameter: metaid_0000016
species: metaid_0000023
volume units: 498095
time units: 949038
units def: metaid_0000007
function def: metaid_0000003
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 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 .
reaction: metaid_0000030
reaction: metaid_0000031
parameter: metaid_0000018

983697
stoichiometry: 1.0
species: metaid_0000022
type: SpeciesReference

983527
stoichiometry: 2.0
species: metaid_0000021
type: SpeciesReference

metaid_0000010
is: SBO:0000009
constant: true
value: 0.5
name: Nt
type: Parameter

metaid_0000017
is: SBO:0000009
constant: true
value: 460.0
name: Kc
type: Parameter

metaid_0000016
is: SBO:0000009
constant: true
value: 2.5
name: kc
type: Parameter

983479
exponent: 1.0
scale: -3
multipler: 1.0
kind: MOLE
type: SBMLUnit

metaid_0000030
name: PGA production - v_c
kinetic law: 983552
reactant: 983515
reactant: 983491
fast: false
type: Reaction
reactant: 983503
product: 983527
reversible: false
modifier: 983539

metaid_0000012
is: SBO:0000009
constant: true
value: 1000.0
name: I
type: Parameter

metaid_0000021
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_0000019
name: PGA
type: Species

metaid_0000011
is: SBO:0000009
constant: true
value: 0.23
name: f
type: Parameter

983588
stoichiometry: 2.0
species: metaid_0000022
type: SpeciesReference