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- PDB-1ir2: Crystal Structure of Activated Ribulose-1,5-bisphosphate Carboxyl... -

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Basic information

Entry
Database: PDB / ID: 1ir2
TitleCrystal Structure of Activated Ribulose-1,5-bisphosphate Carboxylase/oxygenase (Rubisco) from Green alga, Chlamydomonas reinhardtii Complexed with 2-Carboxyarabinitol-1,5-bisphosphate (2-CABP)
Components
  • Large subunit of Rubisco
  • Small subunit of Rubisco
KeywordsLYASE / N-methylmethionine / 4-hydroxyproline / S-methylcysteine / ALPHA/BETA BARREL
Function / homology
Function and homology information


photorespiration / ribulose-bisphosphate carboxylase / ribulose-bisphosphate carboxylase activity / reductive pentose-phosphate cycle / chloroplast stroma / monooxygenase activity / chloroplast / magnesium ion binding
Similarity search - Function
Ribulose bisphosphate carboxylase, small subunit / Ribulose 1,5 Bisphosphate Carboxylase/Oxygenase / Ribulose bisphosphate carboxylase, small subunit / Ribulose bisphosphate carboxylase, large subunit, C-terminal domain / RuBisCO large subunit, N-terminal domain / Ribulose bisphosphate carboxylase small subunit, domain / Ribulose bisphosphate carboxylase, small subunit superfamily / Ribulose bisphosphate carboxylase, small chain / Ribulose bisphosphate carboxylase, small chain / Ribulose bisphosphate carboxylase large subunit, type I ...Ribulose bisphosphate carboxylase, small subunit / Ribulose 1,5 Bisphosphate Carboxylase/Oxygenase / Ribulose bisphosphate carboxylase, small subunit / Ribulose bisphosphate carboxylase, large subunit, C-terminal domain / RuBisCO large subunit, N-terminal domain / Ribulose bisphosphate carboxylase small subunit, domain / Ribulose bisphosphate carboxylase, small subunit superfamily / Ribulose bisphosphate carboxylase, small chain / Ribulose bisphosphate carboxylase, small chain / Ribulose bisphosphate carboxylase large subunit, type I / Ribulose bisphosphate carboxylase, large chain, active site / Ribulose bisphosphate carboxylase large chain active site. / Ribulose bisphosphate carboxylase, large subunit, ferrodoxin-like N-terminal / Ribulose bisphosphate carboxylase large chain, N-terminal domain / Ribulose bisphosphate carboxylase, large subunit, C-terminal / RuBisCO / Ribulose bisphosphate carboxylase, large subunit, C-terminal domain superfamily / RuBisCO large subunit, N-terminal domain superfamily / Ribulose bisphosphate carboxylase large chain, catalytic domain / Alpha-Beta Plaits / TIM Barrel / Alpha-Beta Barrel / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
2-CARBOXYARABINITOL-1,5-DIPHOSPHATE / Ribulose bisphosphate carboxylase large chain / Ribulose bisphosphate carboxylase small subunit, chloroplastic 2
Similarity search - Component
Biological speciesChlamydomonas reinhardtii (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.84 Å
AuthorsMizohata, E. / Matsumura, H. / Okano, Y. / Kumei, M. / Takuma, H. / Onodera, J. / Kato, K. / Shibata, N. / Inoue, T. / Yokota, A. / Kai, Y.
CitationJournal: J.Mol.Biol. / Year: 2002
Title: Crystal structure of activated ribulose-1,5-bisphosphate carboxylase/oxygenase from green alga Chlamydomonas reinhardtii complexed with 2-carboxyarabinitol-1,5-bisphosphate.
Authors: Mizohata, E. / Matsumura, H. / Okano, Y. / Kumei, M. / Takuma, H. / Onodera, J. / Kato, K. / Shibata, N. / Inoue, T. / Yokota, A. / Kai, Y.
History
DepositionSep 3, 2001Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 20, 2002Provider: repository / Type: Initial release
Revision 1.1Jan 8, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 25, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_conn_type / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Large subunit of Rubisco
I: Small subunit of Rubisco
B: Large subunit of Rubisco
J: Small subunit of Rubisco
C: Large subunit of Rubisco
K: Small subunit of Rubisco
D: Large subunit of Rubisco
L: Small subunit of Rubisco
E: Large subunit of Rubisco
M: Small subunit of Rubisco
F: Large subunit of Rubisco
N: Small subunit of Rubisco
G: Large subunit of Rubisco
O: Small subunit of Rubisco
H: Large subunit of Rubisco
P: Small subunit of Rubisco
S: Large subunit of Rubisco
1: Small subunit of Rubisco
T: Large subunit of Rubisco
2: Small subunit of Rubisco
U: Large subunit of Rubisco
3: Small subunit of Rubisco
V: Large subunit of Rubisco
4: Small subunit of Rubisco
W: Large subunit of Rubisco
5: Small subunit of Rubisco
X: Large subunit of Rubisco
6: Small subunit of Rubisco
Y: Large subunit of Rubisco
7: Small subunit of Rubisco
Z: Large subunit of Rubisco
8: Small subunit of Rubisco
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,113,893104
Polymers1,104,12232
Non-polymers9,77072
Water180,1329999
1
A: Large subunit of Rubisco
I: Small subunit of Rubisco
B: Large subunit of Rubisco
J: Small subunit of Rubisco
C: Large subunit of Rubisco
K: Small subunit of Rubisco
D: Large subunit of Rubisco
L: Small subunit of Rubisco
E: Large subunit of Rubisco
M: Small subunit of Rubisco
F: Large subunit of Rubisco
N: Small subunit of Rubisco
G: Large subunit of Rubisco
O: Small subunit of Rubisco
H: Large subunit of Rubisco
P: Small subunit of Rubisco
hetero molecules


Theoretical massNumber of molelcules
Total (without water)556,94652
Polymers552,06116
Non-polymers4,88536
Water28816
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area123440 Å2
ΔGint-617 kcal/mol
Surface area115880 Å2
MethodPISA, PQS
2
S: Large subunit of Rubisco
1: Small subunit of Rubisco
T: Large subunit of Rubisco
2: Small subunit of Rubisco
U: Large subunit of Rubisco
3: Small subunit of Rubisco
V: Large subunit of Rubisco
4: Small subunit of Rubisco
W: Large subunit of Rubisco
5: Small subunit of Rubisco
X: Large subunit of Rubisco
6: Small subunit of Rubisco
Y: Large subunit of Rubisco
7: Small subunit of Rubisco
Z: Large subunit of Rubisco
8: Small subunit of Rubisco
hetero molecules


Theoretical massNumber of molelcules
Total (without water)556,94652
Polymers552,06116
Non-polymers4,88536
Water28816
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area123270 Å2
ΔGint-611 kcal/mol
Surface area116460 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)129.17, 174.75, 222.27
Angle α, β, γ (deg.)90.00, 97.75, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe biological assembly is a hexadecamer comprised of 8 large and 8 small subunits. Two hexadecamer exist in the asymmetric unit.

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Components

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Protein , 2 types, 32 molecules ABCDEFGHSTUVWXYZIJKLMNOP12345678

#1: Protein
Large subunit of Rubisco / RIBULOSE BISPHOSPHATE CARBOXYLASE LARGE CHAIN


Mass: 52696.840 Da / Num. of mol.: 16 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / Strain: 137C mt+
References: UniProt: P00877, ribulose-bisphosphate carboxylase
#2: Protein
Small subunit of Rubisco / RIBULOSE BISPHOSPHATE CARBOXYLASE SMALL CHAIN 2


Mass: 16310.790 Da / Num. of mol.: 16 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / Strain: 137C mt+
References: UniProt: P08475, ribulose-bisphosphate carboxylase

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Sugars , 1 types, 16 molecules

#4: Sugar
ChemComp-CAP / 2-CARBOXYARABINITOL-1,5-DIPHOSPHATE


Type: saccharide / Mass: 356.115 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C6H14O13P2

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Non-polymers , 3 types, 10055 molecules

#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: Mg
#5: Chemical...
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 40 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 9999 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsThere is a DIFFERENCE between seqres(PRO46) and sequence database(LEU46) in LARGE SUBUNIT. THERE IS ...There is a DIFFERENCE between seqres(PRO46) and sequence database(LEU46) in LARGE SUBUNIT. THERE IS NO QUESTION FROM THE ELECTRON DENSITY THAT the 46th residue is PRO.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.25 Å3/Da / Density % sol: 45.34 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: PEG4000, HEPES-KOH, glycerol, NaHCO3, MgCl2, DTT, 2-carboxyarabinitol-1,5-bisphosphate (2-CABP), EDTA, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 20 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
180 mMHEPES-KOH1droppH8.0
21 mMEDTA1drop
35 mMdithiothreitol1drop
420 mM1dropMgCl2
540 mM1dropNaHCO3
625 mg/mlprotein1drop
780 mMHEPES-KOH1reservoirpH8.0
81 mMEDTA1reservoir
920 mM1reservoirMgCl2
106-7 %PEG40001reservoir
1130 %(v/v)glycerol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-18B / Wavelength: 1 Å
DetectorType: WEISSENBERG / Detector: DIFFRACTOMETER / Date: Jun 9, 2000
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.84→40 Å / Num. obs: 763078 / % possible obs: 91 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.068
Reflection shellResolution: 1.84→1.91 Å / Rmerge(I) obs: 0.229 / Num. unique all: 60785 / % possible all: 72.7
Reflection
*PLUS
Lowest resolution: 40 Å / Num. measured all: 4698187
Reflection shell
*PLUS
% possible obs: 72.7 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ID: 1BUR

1bur
PDB Unreleased entry


Resolution: 1.84→39.89 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.181 37921 5 %Random
Rwork0.152 ---
obs-762301 90.6 %-
Displacement parametersBiso mean: 16.1 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.196 Å0.165 Å
Luzzati d res low-5 Å
Luzzati sigma a0.222 Å0.212 Å
Refinement stepCycle: LAST / Resolution: 1.84→39.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms76496 0 592 9999 87087
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.32
X-RAY DIFFRACTIONc_dihedral_angle_deg22.89
X-RAY DIFFRACTIONc_improper_angle_deg0.76
LS refinement shellResolution: 1.84→1.91 Å / Rfactor Rfree error: 0.005
RfactorNum. reflection% reflection
Rfree0.261 2859 -
Rwork0.245 --
obs-58120 69.2 %
Refinement
*PLUS
% reflection Rfree: 5 % / Rfactor obs: 0.152
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 16.1 Å2
LS refinement shell
*PLUS
Rfactor Rfree: 0.261 / Rfactor Rwork: 0.245 / Rfactor obs: 0.245

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