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- PDB-1ir1: Crystal Structure of Spinach Ribulose-1,5-Bisphosphate Carboxylas... -

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Basic information

Entry
Database: PDB / ID: 1ir1
TitleCrystal Structure of Spinach Ribulose-1,5-Bisphosphate Carboxylase/Oxygenase (Rubisco) Complexed with CO2, Mg2+ and 2-Carboxyarabinitol-1,5-Bisphosphate
Components
  • Large subunit of Rubisco
  • Small subunit of Rubisco
KeywordsLYASE / ALPHA/BETA BARREL
Function / homology
Function and homology information


photorespiration / ribulose-bisphosphate carboxylase / ribulose-bisphosphate carboxylase activity / reductive pentose-phosphate cycle / chloroplast / monooxygenase activity / magnesium ion binding
Similarity search - Function
Ribulose-1,5-bisphosphate carboxylase small subunit, N-terminal / Ribulose-1,5-bisphosphate carboxylase small subunit / Ribulose bisphosphate carboxylase, small subunit / Ribulose 1,5 Bisphosphate Carboxylase/Oxygenase / RuBisCO large subunit, N-terminal domain / Ribulose bisphosphate carboxylase, large subunit, C-terminal domain / Ribulose bisphosphate carboxylase, small subunit / Ribulose bisphosphate carboxylase small subunit, domain / Ribulose bisphosphate carboxylase, small subunit superfamily / Ribulose bisphosphate carboxylase, small chain ...Ribulose-1,5-bisphosphate carboxylase small subunit, N-terminal / Ribulose-1,5-bisphosphate carboxylase small subunit / Ribulose bisphosphate carboxylase, small subunit / Ribulose 1,5 Bisphosphate Carboxylase/Oxygenase / RuBisCO large subunit, N-terminal domain / Ribulose bisphosphate carboxylase, large subunit, C-terminal domain / Ribulose bisphosphate carboxylase, small subunit / 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 speciesSpinacia oleracea (spinach)
MethodX-RAY DIFFRACTION / SYNCHROTRON / RE-REFINEMENT of 1BUR / Resolution: 1.8 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
DepositionAug 31, 2001Deposition site: PDBJ / Processing site: PDBJ
SupersessionMar 13, 2002ID: 1BUR
Revision 1.0Mar 13, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 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
S: Small subunit of Rubisco
B: Large subunit of Rubisco
T: Small subunit of Rubisco
C: Large subunit of Rubisco
U: Small subunit of Rubisco
D: Large subunit of Rubisco
V: Small subunit of Rubisco
hetero molecules


Theoretical massNumber of molelcules
Total (without water)271,67116
Polymers270,1508
Non-polymers1,5228
Water40,9302272
1
A: Large subunit of Rubisco
S: Small subunit of Rubisco
B: Large subunit of Rubisco
T: Small subunit of Rubisco
C: Large subunit of Rubisco
U: Small subunit of Rubisco
D: Large subunit of Rubisco
V: Small subunit of Rubisco
hetero molecules

A: Large subunit of Rubisco
S: Small subunit of Rubisco
B: Large subunit of Rubisco
T: Small subunit of Rubisco
C: Large subunit of Rubisco
U: Small subunit of Rubisco
D: Large subunit of Rubisco
V: Small subunit of Rubisco
hetero molecules


Theoretical massNumber of molelcules
Total (without water)543,34332
Polymers540,30016
Non-polymers3,04316
Water28816
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area110760 Å2
ΔGint-503 kcal/mol
Surface area120160 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)157.8, 157.8, 200.9
Angle α, β, γ (deg.)90, 90, 90
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11B-534-

HOH

21B-714-

HOH

31B-716-

HOH

41B-765-

HOH

51D-518-

HOH

61D-521-

HOH

71D-524-

HOH

81D-716-

HOH

91D-798-

HOH

101D-800-

HOH

111D-841-

HOH

DetailsThe biological assembly is a hexadecamer comprised of 8 large and 8 small subunits. A half of the hexadecamer (4 large and 4 small subunits) exists in the asymmetric unit. The rest part is generated by -x, y, -z+1/2.

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Components

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


Mass: 52849.742 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / Organ: leaves
References: UniProt: P00875, ribulose-bisphosphate carboxylase
#2: Protein
Small subunit of Rubisco / RIBULOSE BISPHOSPHATE CARBOXYLASE SMALL CHAIN 2


Mass: 14687.708 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / Organ: leaves
References: UniProt: Q43832, ribulose-bisphosphate carboxylase
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#4: Sugar
ChemComp-CAP / 2-CARBOXYARABINITOL-1,5-DIPHOSPHATE


Type: saccharide / Mass: 356.115 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H14O13P2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2272 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 2.31 Å3/Da / Density % sol: 46.84 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7.9
Details: PEG4000, MgCl2, NaHCO3, DTT, 2-carboxyarabinitol-1,5-bisphosphate, Bicine, pH 7.9, VAPOR DIFFUSION, temperature 293K
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 8 / Method: vapor diffusion, hanging drop
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: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A
DetectorType: WEISSENBERG / Detector: DIFFRACTOMETER
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.8→10 Å / Num. obs: 175568 / % possible obs: 76.9 %
Reflection shellResolution: 1.8→1.86 Å / Num. unique all: 10760 / % possible all: 47.5

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Processing

SoftwareName: CNS / Version: 1 / Classification: refinement
RefinementMethod to determine structure: RE-REFINEMENT of 1BUR
Starting model: PDB ID 1BUR

1bur
PDB Unreleased entry


Resolution: 1.8→10 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.179 8801 5 %RANDOM
Rwork0.155 ---
obs-175568 76.9 %-
Refine analyze
FreeObs
Luzzati coordinate error0.203 Å0.176 Å
Luzzati d res low-5 Å
Luzzati sigma a0.278 Å0.244 Å
Refinement stepCycle: LAST / Resolution: 1.8→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18696 0 88 2272 21056
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.36
X-RAY DIFFRACTIONc_dihedral_angle_deg23.42
X-RAY DIFFRACTIONc_improper_angle_deg0.81
LS refinement shellResolution: 1.8→1.86 Å / Rfactor Rfree error: 0.013
RfactorNum. reflection% reflection
Rfree0.304 573 -
Rwork0.282 --
obs-10760 47.5 %
Refinement
*PLUS
Rfactor Rfree: 0.179 / Rfactor Rwork: 0.155
Solvent computation
*PLUS
Displacement parameters
*PLUS
LS refinement shell
*PLUS
Highest resolution: 1.8 Å / Rfactor Rfree: 0.304 / Rfactor Rwork: 0.282

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