BIOMD0000000386
type: SBMLModel
reaction: metaid_0000039
species: metaid_0000024
creator:
  ORG:
    orgname: Institute of Biochemistry and Biology, University of Potsdam, 14476 Potsdam, Germany
  n:
    given: Zoran
    family: Nikoloski
name: Oxygenation
parameter: metaid_0000009
name: NADPH production
creator:
  ORG:
    orgname: Max-Planck-Institute of Molecular Plant Physiology
  n:
    given: Anne
    family: Arnold
compartment: metaid_0000023
rule: metaid_0000032
parameter: metaid_0000012
parameter: metaid_0000018
is: GO:0019253
rule: metaid_0000035
parameter: metaid_0000017
area units: 498119
species: metaid_0000028
is described by: http://identifiers.org/pubmed/22001849
name: Arnold2011_Sharkey2007_RuBisCO-CalvinCycle
species: metaid_0000025
substance units: metaid_0000007
reaction: metaid_0000038
parameter: metaid_0000022
name: PGA consumption
reaction: metaid_0000037
parameter: metaid_0000015
name: Carboxylation
function def: metaid_0000006
creator:
  ORG:
    orgname: EMBL-EBI
  n:
    given: Vijayalakshmi
    family: Chelliah
rule: metaid_0000033
occurs in: http://identifiers.org/taxonomy/33090
species: metaid_0000029
function def: metaid_0000004
parameter: metaid_0000016
curated: true
modified:
  W3 CDTF: Fri Apr 20 20:52:27 BST 2012
volume units: 498095
species: metaid_0000026
parameter: metaid_0000011
rule: metaid_0000030
parameter: metaid_0000021
is: MODEL1109270002
reaction: metaid_0000036
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 Sharkey et al. (2007, DOI:10.1111/j.1365-3040.2007.01710.x ). The parameter values are partly taken from Farquhar et al. (1980,DOI:10.1007/BF00386231 ) and Medlyn et al. (2002,DOI:10.1046/j.1365-3040.2002.00891.x ). 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_0000014
parameter: metaid_0000020
created:
  W3 CDTF: Wed Oct 19 15:51:41 BST 2011
units def: metaid_0000007
parameter: metaid_0000013
parameter: metaid_0000019
rule: metaid_0000034
function def: metaid_0000005
parameter: metaid_0000008
length unit: length
time units: 949038
species: metaid_0000027
function def: metaid_0000003
parameter: metaid_0000010
rule: metaid_0000031

metaid_0000039
type: Reaction
kinetic law: 022491
product: 022479
reactant: 022467
fast: false
reversible: false
name: NADPH production

022479
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000026

metaid_0000026
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_0000023
name: NADPH

metaid_0000023
type: Compartment
constant: true
size: 1.0
spatial dimensions: 3.0
name: chloroplast

022467
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000029

metaid_0000029
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_0000023
name: NADP

metaid_0000024
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_0000023
name: RuBP

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

metaid_0000012
type: Parameter
notes: converted into [mM] using Winter et al. (1994) subcellular stroma volume, BioNumbers (ID: 105594)
is: SBO:0000009
constant: true
value: 0.0307740792044142
name: gm

metaid_0000018
type: Parameter
notes: converted into [mM] using Winter et al. (1994) subcellular stroma volume, BioNumbers (ID: 105594)
is: SBO:0000196
constant: true
value: 0.0307585098788555
name: TPU

metaid_0000017
type: Parameter
is: SBO:0000009
constant: false
value: 0.286292104000314
name: phi

metaid_0000028
type: Species
constant: true
has only substance units: false
name: O2
initial concentration: 21.0
notes: [kPa]
initial amount: NaN
boundary condition: true
in compartment: metaid_0000023
is version of: CHEBI:15379

metaid_0000025
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_0000023
name: PGA

022263
type: SBMLUnit
exponent: 1.0
scale: -3
multipler: 1.0
kind: MOLE

metaid_0000038
type: Reaction
kinetic law: 022455
modifier: 022443
product: 022431
reactant: 022419
fast: false
reversible: false
name: PGA consumption

022431
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000024

022419
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000025

metaid_0000022
type: Parameter
notes: incorporates assimilation rate (A) dependence; solved and replaced (causes a complex assignment)
is: SBO:0000009
constant: false
value: 0.00892944491541968
name: Vc

metaid_0000037
type: Reaction
modifier: 022395
reversible: false
reactant: 022359
product: 022383
reactant: 022347
name: PGA production - v_o
kinetic law: 022407
fast: false
reactant: 022371

metaid_0000027
type: Species
has only substance units: false
is version of: CHEBI:16526
initial concentration: 24.5
name: CO2
in compartment: metaid_0000023
initial amount: NaN
boundary condition: true
notes: [Pa]
constant: true

022359
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000028

022383
type: SpeciesReference
stoichiometry: 1.5
species: metaid_0000025

022347
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000024

022371
type: SpeciesReference
stoichiometry: 2.0
species: metaid_0000026

metaid_0000015
type: Parameter
is: SBO:0000009
constant: true
value: 27.2372124161502
name: Kc

metaid_0000016
type: Parameter
is: SBO:0000009
constant: true
value: 16.5788431231261
name: Ko

metaid_0000011
type: Parameter
notes: converted into [mM] using Winter et al. (1994) subcellular stroma volume, BioNumbers (ID: 105594)
is: SBO:0000009
constant: true
value: 0.0307678189755062
name: J

metaid_0000021
type: Parameter
notes: incorporates assimilation rate (A) dependence; solved and replaced (causes a complex assignment)
is: SBO:0000009
constant: false
value: 0.110677228404984
name: Vp

metaid_0000036
type: Reaction
reactant: 022299
modifier: 022323
product: 022311
kinetic law: 022335
reactant: 022275
reactant: 022287
fast: false
name: PGA production - v_c
reversible: false

022299
type: SpeciesReference
stoichiometry: 2.0
species: metaid_0000026

022311
type: SpeciesReference
stoichiometry: 2.0
species: metaid_0000025

022275
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000024

022287
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000027

metaid_0000014
type: Parameter
notes: converted into [mM] using Winter et al. (1994) subcellular stroma volume, BioNumbers (ID: 105594)
is: SBO:0000009
constant: true
value: 0.0307602623029146
name: Vcmax

metaid_0000020
type: Parameter
notes: incorporates assimilation rate (A) dependence; solved and replaced (causes a complex assignment)
is: SBO:0000009
constant: false
value: 0.00593820961819415
name: Vj

metaid_0000013
type: Parameter
is: SBO:0000009
constant: true
value: 3.74116898182615
name: Gamma

metaid_0000019
type: Parameter
is: SBO:0000009
constant: false
value: 0.00593820961819415
name: v_c

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

metaid_0000010
type: Parameter
notes: converted into [mM] using Winter et al. (1994) subcellular stroma volume, BioNumbers (ID: 105594)
is: SBO:0000009
constant: true
value: 0.0307674936008629
name: Rd