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- PDB-1aa1: ACTIVATED SPINACH RUBISCO IN COMPLEX WITH THE PRODUCT 3-PHOSPHOGL... -

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Basic information

Entry
Database: PDB / ID: 1aa1
TitleACTIVATED SPINACH RUBISCO IN COMPLEX WITH THE PRODUCT 3-PHOSPHOGLYCERATE
Components
  • RIBULOSE BISPHOSPHATE CARBOXYLASE (LARGE CHAIN)
  • RIBULOSE BISPHOSPHATE CARBOXYLASE (SMALL CHAIN)
KeywordsOXIDOREDUCTASE / LYASE (CARBON-CARBON)
Function / homology
Function and homology information


photorespiration / ribulose-bisphosphate carboxylase / ribulose-bisphosphate carboxylase activity / reductive pentose-phosphate cycle / monooxygenase activity / chloroplast / 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 / 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-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 / 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
3-PHOSPHOGLYCERIC ACID / Ribulose bisphosphate carboxylase large chain / Ribulose bisphosphate carboxylase small subunit, chloroplastic 2
Similarity search - Component
Biological speciesSpinacia oleracea (spinach)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.2 Å
AuthorsTaylor, T.C. / Andersson, I.
Citation
Journal: Biochemistry / Year: 1997
Title: Structure of a product complex of spinach ribulose-1,5-bisphosphate carboxylase/oxygenase.
Authors: Taylor, T.C. / Andersson, I.
#1: Journal: J.Mol.Biol. / Year: 1996
Title: Large Structures at High Resolution: The 1.6 A Crystal Structure of Spinach Ribulose-1,5-Bisphosphate Carboxylase/Oxygenase Complexed with 2-Carboxyarabinitol Bisphosphate
Authors: Andersson, I.
History
DepositionJan 20, 1997Processing site: BNL
Revision 1.0Jul 7, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Jun 5, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_conn_angle / pdbx_struct_special_symmetry / struct_conn / 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 / _pdbx_database_status.process_site / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: RIBULOSE BISPHOSPHATE CARBOXYLASE (LARGE CHAIN)
S: RIBULOSE BISPHOSPHATE CARBOXYLASE (SMALL CHAIN)
B: RIBULOSE BISPHOSPHATE CARBOXYLASE (LARGE CHAIN)
C: RIBULOSE BISPHOSPHATE CARBOXYLASE (SMALL CHAIN)
E: RIBULOSE BISPHOSPHATE CARBOXYLASE (LARGE CHAIN)
F: RIBULOSE BISPHOSPHATE CARBOXYLASE (SMALL CHAIN)
H: RIBULOSE BISPHOSPHATE CARBOXYLASE (LARGE CHAIN)
I: RIBULOSE BISPHOSPHATE CARBOXYLASE (SMALL CHAIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)271,25120
Polymers269,6658
Non-polymers1,58612
Water18,1591008
1
L: RIBULOSE BISPHOSPHATE CARBOXYLASE (LARGE CHAIN)
S: RIBULOSE BISPHOSPHATE CARBOXYLASE (SMALL CHAIN)
B: RIBULOSE BISPHOSPHATE CARBOXYLASE (LARGE CHAIN)
C: RIBULOSE BISPHOSPHATE CARBOXYLASE (SMALL CHAIN)
E: RIBULOSE BISPHOSPHATE CARBOXYLASE (LARGE CHAIN)
F: RIBULOSE BISPHOSPHATE CARBOXYLASE (SMALL CHAIN)
H: RIBULOSE BISPHOSPHATE CARBOXYLASE (LARGE CHAIN)
I: RIBULOSE BISPHOSPHATE CARBOXYLASE (SMALL CHAIN)
hetero molecules

L: RIBULOSE BISPHOSPHATE CARBOXYLASE (LARGE CHAIN)
S: RIBULOSE BISPHOSPHATE CARBOXYLASE (SMALL CHAIN)
B: RIBULOSE BISPHOSPHATE CARBOXYLASE (LARGE CHAIN)
C: RIBULOSE BISPHOSPHATE CARBOXYLASE (SMALL CHAIN)
E: RIBULOSE BISPHOSPHATE CARBOXYLASE (LARGE CHAIN)
F: RIBULOSE BISPHOSPHATE CARBOXYLASE (SMALL CHAIN)
H: RIBULOSE BISPHOSPHATE CARBOXYLASE (LARGE CHAIN)
I: RIBULOSE BISPHOSPHATE CARBOXYLASE (SMALL CHAIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)542,50240
Polymers539,33116
Non-polymers3,17124
Water28816
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area102510 Å2
ΔGint-473 kcal/mol
Surface area116560 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)157.600, 158.700, 203.300
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11B-488-

HOH

21B-622-

HOH

31B-654-

HOH

41H-493-

HOH

51H-656-

HOH

Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.0007, 1, -0.000314), (-0.999999, 0.0007, 0.001214), (0.001214, 0.000314, 0.999999)-37.6482, 37.5401, 0.084
2given(-0.999977, -0.000876, 0.006737), (0.00089, -0.999997, 0.002166), (0.006735, 0.002172, 0.999975)-0.2549, 75.2133, 0.0242
3given(-0.001857, -0.999994, 0.00299), (0.999998, -0.001858, -0.000389), (0.000395, 0.00299, 0.999995)37.4344, 37.788, -0.1172

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Components

#1: Protein
RIBULOSE BISPHOSPHATE CARBOXYLASE (LARGE CHAIN) / RUBISCO


Mass: 52777.680 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / Organ: LEAF
References: UniProt: P00875, ribulose-bisphosphate carboxylase
#2: Protein
RIBULOSE BISPHOSPHATE CARBOXYLASE (SMALL CHAIN) / RUBISCO


Mass: 14638.671 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / Organ: LEAF
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: Chemical
ChemComp-3PG / 3-PHOSPHOGLYCERIC ACID


Mass: 186.057 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H7O7P
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1008 / 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: 7

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Sample preparation

CrystalDensity Matthews: 2.36 Å3/Da / Density % sol: 40 %
Crystal growpH: 7.2
Details: 14% PEG 4000, 0.2 M NACL, 25 MM HEPES PH 7.8 10 MM MGCL2, 100 MM 3-PHOSPHOGLYCERATE, pH 7.2
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion, hanging drop / Details: Taylor, T.C., (1996) Nat. Struct. Biol., 3, 95.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
150-60 mg/mlprotein1drop
2100 mM3-PGA1drop
314-16 %PEG40001reservoir
40.2 M1reservoirNaCl
525 mMHEPES1reservoir
610 mM1reservoirMgCl2
750 mM1reservoirNaHCO3
80.02 %1reservoirNaN3

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Data collection

DiffractionMean temperature: 283 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.5 / Wavelength: 0.87
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 1, 1994
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 2.2→20 Å / Num. obs: 107965 / % possible obs: 85 % / Redundancy: 7.4 % / Rmerge(I) obs: 0.103 / Net I/σ(I): 9.8
Reflection shellResolution: 2.2→2.28 Å / Rmerge(I) obs: 0.205 / Mean I/σ(I) obs: 4.7 / % possible all: 75
Reflection
*PLUS
Num. measured all: 799161

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
MOSFLMdata reduction
CCP4data scaling
X-PLOR3.1phasing
RefinementResolution: 2.2→7 Å / Isotropic thermal model: INDIVIDUAL / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.224 3261 3 %RANDOM
Rwork0.207 ---
obs0.207 104308 83.8 %-
Refinement stepCycle: LAST / Resolution: 2.2→7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17856 0 92 1008 18956
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.667
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d22.8
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.256
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Refine LS restraints NCSNCS model details: CONSTRAINTS
LS refinement shellResolution: 2.2→2.3 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.252 293 3 %
Rwork0.261 10188 -
obs--67.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2WAT.PARAWAT.TOP
X-RAY DIFFRACTION3PGA.PARAPGA.TOP
X-RAY DIFFRACTION4CARB.PARACARB.TOP
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg22.8
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.256

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