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- PDB-1rbo: SPINACH RUBISCO IN COMPLEX WITH THE INHIBITOR 2-CARBOXYARABINITOL... -

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Basic information

Entry
Database: PDB / ID: 1rbo
TitleSPINACH RUBISCO IN COMPLEX WITH THE INHIBITOR 2-CARBOXYARABINITOL-1,5-DIPHOSPHATE
Components(RIBULOSE BISPHOSPHATE CARBOXYLASE/OXYGENASE) x 2
KeywordsLYASE / CARBON-CARBON
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 bisphosphate carboxylase, small subunit / Ribulose 1,5 Bisphosphate Carboxylase/Oxygenase / RuBisCO large subunit, N-terminal domain / Ribulose bisphosphate carboxylase, small subunit / Ribulose bisphosphate carboxylase, large subunit, C-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 / RuBisCO large subunit, N-terminal domain / Ribulose bisphosphate carboxylase, small subunit / Ribulose bisphosphate carboxylase, large subunit, C-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 small subunit, chloroplastic 1 / Ribulose bisphosphate carboxylase large chain
Similarity search - Component
Biological speciesSpinacia oleracea (spinach)
MethodX-RAY DIFFRACTION / SYNCHROTRON / ISOMORPHOUS WITH 8RUC / Resolution: 2.3 Å
AuthorsTaylor, T.C. / Andersson, I.
Citation
Journal: J.Biol.Chem. / Year: 1996
Title: A common structural basis for the inhibition of ribulose 1,5-bisphosphate carboxylase by 4-carboxyarabinitol 1,5-bisphosphate and xylulose 1,5-bisphosphate.
Authors: Taylor, T.C. / Fothergill, M.D. / 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
DepositionOct 31, 1996Processing site: BNL
Revision 1.0Mar 12, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 3, 2018Group: Data collection / Derived calculations / Category: diffrn_source / struct_conn
Item: _diffrn_source.pdbx_synchrotron_site / _struct_conn.pdbx_dist_value ..._diffrn_source.pdbx_synchrotron_site / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id
Revision 1.4Oct 23, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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 / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_symmetry / _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/OXYGENASE
S: RIBULOSE BISPHOSPHATE CARBOXYLASE/OXYGENASE
B: RIBULOSE BISPHOSPHATE CARBOXYLASE/OXYGENASE
C: RIBULOSE BISPHOSPHATE CARBOXYLASE/OXYGENASE
E: RIBULOSE BISPHOSPHATE CARBOXYLASE/OXYGENASE
F: RIBULOSE BISPHOSPHATE CARBOXYLASE/OXYGENASE
H: RIBULOSE BISPHOSPHATE CARBOXYLASE/OXYGENASE
I: RIBULOSE BISPHOSPHATE CARBOXYLASE/OXYGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)270,91812
Polymers269,4938
Non-polymers1,4244
Water19,6001088
1
L: RIBULOSE BISPHOSPHATE CARBOXYLASE/OXYGENASE
S: RIBULOSE BISPHOSPHATE CARBOXYLASE/OXYGENASE
B: RIBULOSE BISPHOSPHATE CARBOXYLASE/OXYGENASE
C: RIBULOSE BISPHOSPHATE CARBOXYLASE/OXYGENASE
E: RIBULOSE BISPHOSPHATE CARBOXYLASE/OXYGENASE
F: RIBULOSE BISPHOSPHATE CARBOXYLASE/OXYGENASE
H: RIBULOSE BISPHOSPHATE CARBOXYLASE/OXYGENASE
I: RIBULOSE BISPHOSPHATE CARBOXYLASE/OXYGENASE
hetero molecules

L: RIBULOSE BISPHOSPHATE CARBOXYLASE/OXYGENASE
S: RIBULOSE BISPHOSPHATE CARBOXYLASE/OXYGENASE
B: RIBULOSE BISPHOSPHATE CARBOXYLASE/OXYGENASE
C: RIBULOSE BISPHOSPHATE CARBOXYLASE/OXYGENASE
E: RIBULOSE BISPHOSPHATE CARBOXYLASE/OXYGENASE
F: RIBULOSE BISPHOSPHATE CARBOXYLASE/OXYGENASE
H: RIBULOSE BISPHOSPHATE CARBOXYLASE/OXYGENASE
I: RIBULOSE BISPHOSPHATE CARBOXYLASE/OXYGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)541,83624
Polymers538,98716
Non-polymers2,8498
Water28816
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area111320 Å2
ΔGint-445 kcal/mol
Surface area118520 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)157.200, 157.200, 201.300
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.001291, 0.999448, -0.033197), (-0.999472, 0.000212, -0.032479), (-0.032454, 0.033222, 0.998921)-37.779, 41.0559, -1.2659
2given(-0.997856, 6.1E-5, -0.06545), (-0.000137, -0.999999, 0.001161), (-0.06545, 0.001168, 0.997855)3.2888, 78.885, 0.0535
3given(0.001029, -0.99949, -0.031926), (0.999458, -2.2E-5, 0.032918), (-0.032902, -0.031942, 0.998948)41.0601, 37.8333, 1.3137
DetailsTHE DEPOSITORS PROVIDED CHAINS L AND S. THE OTHER CHAINS TO MAKE THE COMPLETE ASYMMETRIC UNIT WERE GENERATED BY THE PROTEIN DATA BANK USING THE MTRIX TRANSFORMATIONS BELOW.

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Components

#1: Protein
RIBULOSE BISPHOSPHATE CARBOXYLASE/OXYGENASE / RUBISCO


Mass: 52734.680 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/OXYGENASE / 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: P00870, ribulose-bisphosphate carboxylase
#3: Sugar
ChemComp-CAP / 2-CARBOXYARABINITOL-1,5-DIPHOSPHATE


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


Mass: 18.015 Da / Num. of mol.: 1088 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.31 Å3/Da / Density % sol: 40 %
Crystal growpH: 7.4
Details: 1.7 M (NH4)2SO4, 50 MM PHOSPHATE, PH 7.4 3 MM MGCL2, 25 MM NAHCO3, 10 MM 4CABP
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
1100 mg/mlspinach Rubisco1drop
23 mM1dropMgCl2
325 mM1dropNaHCO3
410 mM4-CABP1drop
550 mMphosphate1drop
61.7 Mammonium sulfate1reservoir
750 mMphosphate1reservoir

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Data collection

DiffractionMean temperature: 279 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X31 / Wavelength: 1.009
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 1, 1989
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.009 Å / Relative weight: 1
ReflectionResolution: 2.3→20 Å / Num. obs: 108532 / % possible obs: 90.7 % / Redundancy: 4.5 % / Rmerge(I) obs: 0.059 / Net I/σ(I): 9.8
Reflection shellResolution: 2.3→2.36 Å / % possible all: 100
Reflection
*PLUS
Num. measured all: 488333
Reflection shell
*PLUS
% possible obs: 100 %

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
CCP4data reduction
X-PLOR3.1model building
X-PLOR3.1refinement
CCP4data scaling
X-PLOR3.1phasing
RefinementMethod to determine structure: ISOMORPHOUS WITH 8RUC / Resolution: 2.3→7 Å / Isotropic thermal model: INDIVIDUAL / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.171 5457 5 %RANDOM
Rwork0.154 ---
obs0.154 105190 99.1 %-
Refinement stepCycle: LAST / Resolution: 2.3→7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18728 0 84 1088 19900
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
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_deg1.607
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.4
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: 2.3→2.4 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.178 619 5 %
Rwork0.167 12542 -
obs--100 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2WAT.PARAWAT.TOP
X-RAY DIFFRACTION34CABP.PARA4CABP.TOP
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.4
LS refinement shell
*PLUS
Rfactor obs: 0.167

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