035495
stoichiometry: 1.0
species: metaid_0000026
type: SpeciesReference

metaid_0000017
notes: Bernacchi et al. (2001) Equation (8), Table 1
is: SBO:0000009
constant: true
value: 187891.032274486
name: Ko
type: Parameter

035689
stoichiometry: 1.0
species: metaid_0000031
type: SpeciesReference

metaid_0000013
notes: equals 0.5 O2/tau Urban et al. (2003) (p. 291), Equation (8), Table 1
is: SBO:0000009
constant: false
value: 4.29040862748855
name: Gamma
type: Parameter

035652
stoichiometry: 1.0
species: metaid_0000026
type: SpeciesReference

metaid_0000044
kinetic law: 035714
product: 035701
reactant: 035689
fast: false
reversible: false
name: NADPH production
type: Reaction

metaid_0000030
name: O2
initial concentration: 21000.0
has only substance units: false
notes: [Pa]
boundary condition: true
constant: true
is version of: CHEBI:15379
type: Species
in compartment: metaid_0000025
initial amount: NaN

metaid_0000010
notes: Urban et al. (2003) Table 1
is: SBO:0000009
constant: true
value: 0.24
name: alpha
type: Parameter

metaid_0000027
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_0000025
name: PGA
type: Species

metaid_0000020
is: SBO:0000009
constant: false
value: 0.822489884906092
name: Vc
type: Parameter

035604
stoichiometry: 1.5
species: metaid_0000027
type: SpeciesReference

metaid_0000016
notes: Bernacchi et al. (2001) Equation (8), Table 1
is: SBO:0000009
constant: true
value: 26.7125313821435
name: Kc
type: Parameter

metaid_0000012
notes: Harley et al. (1992) Equation (9), Table 1
is: SBO:0000009
constant: true
value: 142.047003854271
name: Jmax
type: Parameter

metaid_0000041
name: PGA production - v_c
reactant: 035519
reactant: 035495
fast: false
reversible: false
reactant: 035507
modifier: 035543
kinetic law: 035556
product: 035531
type: Reaction

BIOMD0000000387
is: MODEL1109270003
rule: metaid_0000033
species: metaid_0000031
creator:
  ORG:
    orgname: Max-Planck-Institute of Molecular Plant Physiology
  n:
    given: Anne
    family: Arnold
name: Oxygenation
rule: metaid_0000040
species: metaid_0000030
reaction: metaid_0000043
species: metaid_0000028
parameter: metaid_0000013
parameter: metaid_0000019
parameter: metaid_0000021
species: metaid_0000027
name: Arnold2011_Damour2007_RuBisCO-CalvinCycle
parameter: metaid_0000008
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 Damour and Urban (2007, [for PDF click here] ). The parameter values are partly taken from Farquhar et al. (1980,DOI:10.1007/BF00386231 ) and Urban et al. (2003,DOI:10.1093/treephys/23.5.289 ). 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 .
units def: metaid_0000007
substance units: metaid_0000007
parameter: metaid_0000016
name: NADPH production
name: Carboxylation
volume units: 498095
modified:
  W3 CDTF: Fri Apr 20 20:52:02 BST 2012
time units: 949038
function def: metaid_0000006
is described by: http://identifiers.org/pubmed/22001849
parameter: metaid_0000010
creator:
  ORG:
    orgname: Institute of Biochemistry and Biology, University of Potsdam, 14476 Potsdam, Germany
  n:
    given: Zoran
    family: Nikoloski
parameter: metaid_0000014
function def: metaid_0000004
parameter: metaid_0000022
creator:
  ORG:
    orgname: EMBL-EBI
  n:
    given: Vijayalakshmi
    family: Chelliah
function def: metaid_0000003
parameter: metaid_0000009
rule: metaid_0000038
reaction: metaid_0000041
species: metaid_0000026
rule: metaid_0000039
rule: metaid_0000035
parameter: metaid_0000017
reaction: metaid_0000044
parameter: metaid_0000011
species: metaid_0000032
parameter: metaid_0000015
parameter: metaid_0000023
rule: metaid_0000034
species: metaid_0000029
function def: metaid_0000005
compartment: metaid_0000025
rule: metaid_0000037
rule: metaid_0000036
reaction: metaid_0000042
parameter: metaid_0000012
parameter: metaid_0000018
area units: 498119
parameter: metaid_0000020
length unit: length
parameter: metaid_0000024
type: SBMLModel
occurs in: http://identifiers.org/taxonomy/33090
name: PGA consumption
encodes: GO:0019253
created:
  W3 CDTF: Wed Oct 19 15:52:11 BST 2011
curated: true

metaid_0000031
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_0000025
name: NADP
type: Species

metaid_0000026
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_0000025
name: RuBP
type: Species

035519
stoichiometry: 2.0
species: metaid_0000028
type: SpeciesReference

metaid_0000011
notes: converted into [mM] using Winter et al. (1994) subcellular stroma volume, BioNumbers (ID: 105594)
is: SBO:0000009
constant: false
value: 3.64863790509821
name: J
type: Parameter

035531
stoichiometry: 2.0
species: metaid_0000027
type: SpeciesReference

metaid_0000021
is: SBO:0000009
constant: false
value: 0.942054655190967
name: Vp
type: Parameter

035592
stoichiometry: 2.0
species: metaid_0000028
type: SpeciesReference

035701
stoichiometry: 1.0
species: metaid_0000028
type: SpeciesReference

metaid_0000032
boundary condition: true
is version of: CHEBI:28017
notes: [g/m²]
initial concentration: 0.5
constant: true
in compartment: metaid_0000025
initial amount: NaN
type: Species
name: starch
has only substance units: false

metaid_0000019
is: SBO:0000009
constant: false
value: 0.025590660664217
name: phi
type: Parameter

035640
stoichiometry: 1.0
species: metaid_0000027
type: SpeciesReference

metaid_0000042
product: 035604
kinetic law: 035628
fast: false
modifier: 035616
reactant: 035592
name: PGA production - v_o
reactant: 035568
reactant: 035580
reversible: false
type: Reaction

035568
stoichiometry: 1.0
species: metaid_0000026
type: SpeciesReference

035483
exponent: 1.0
scale: -3
multipler: 1.0
kind: MOLE
type: SBMLUnit

metaid_0000015
notes: Harley et al. (1992) Equation (9), Table 1; converted into [mM] using Winter et al. (1994) subcellular stroma volume, BioNumbers (ID: 105594)
is: SBO:0000009
constant: true
value: 1.91141270310584
name: Vcmax
type: Parameter

metaid_0000025
constant: true
size: 1.0
spatial dimensions: 3.0
name: chloroplast
type: Compartment

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

metaid_0000029
constant: true
initial concentration: 24.5
initial amount: NaN
type: Species
in compartment: metaid_0000025
name: CO2
has only substance units: false
is version of: CHEBI:16526
boundary condition: true
notes: [Pa]

metaid_0000022
notes: Harley et al. (1992) Equation (9), Table 1; converted into [mM] using Winter et al. (1994) subcellular stroma volume, BioNumbers (ID: 105594)
is: SBO:0000196
constant: true
value: 0.259027750094988
name: TPU
type: Parameter

metaid_0000018
is: SBO:0000009
constant: false
value: 0.675554869049198
name: Vj
type: Parameter

035580
stoichiometry: 1.0
species: metaid_0000030
type: SpeciesReference

metaid_0000043
kinetic law: 035677
modifier: 035664
product: 035652
reactant: 035640
fast: false
reversible: false
name: PGA consumption
type: Reaction

metaid_0000014
is: SBO:0000009
constant: true
value: 1000.0
name: Q
type: Parameter

metaid_0000024
notes: Urban et al. (2007) (p. 348)
is: SBO:0000009
constant: true
value: 0.0434
name: a
type: Parameter

metaid_0000008
is: SBO:0000009
constant: true
value: 3.2
name: Rp
type: Parameter

metaid_0000023
is: SBO:0000009
constant: false
value: 0.999136712846952
name: Cst
type: Parameter

035507
stoichiometry: 1.0
species: metaid_0000029
type: SpeciesReference

metaid_0000028
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_0000025
name: NADPH
type: Species