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- PDB-1rco: SPINACH RUBISCO IN COMPLEX WITH THE INHIBITOR D-XYLULOSE-2,2-DIOL... -

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Basic information

Entry
Database: PDB / ID: 1rco
TitleSPINACH RUBISCO IN COMPLEX WITH THE INHIBITOR D-XYLULOSE-2,2-DIOL-1,5-BISPHOSPHATE
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, 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, 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
D-XYLULOSE-2,2-DIOL-1,5-BISPHOSPHATE / Ribulose bisphosphate carboxylase small subunit, chloroplastic 1 / Ribulose bisphosphate carboxylase large chain
Similarity search - Component
Biological speciesSpinacia oleracea (spinach)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / 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: Version format compliance
Revision 1.3Aug 9, 2023Group: Database references / Derived calculations / Refinement description
Category: database_2 / pdbx_initial_refinement_model ...database_2 / pdbx_initial_refinement_model / 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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 30, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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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
K: RIBULOSE BISPHOSPHATE CARBOXYLASE/OXYGENASE
M: RIBULOSE BISPHOSPHATE CARBOXYLASE/OXYGENASE
O: RIBULOSE BISPHOSPHATE CARBOXYLASE/OXYGENASE
P: RIBULOSE BISPHOSPHATE CARBOXYLASE/OXYGENASE
R: RIBULOSE BISPHOSPHATE CARBOXYLASE/OXYGENASE
T: RIBULOSE BISPHOSPHATE CARBOXYLASE/OXYGENASE
V: RIBULOSE BISPHOSPHATE CARBOXYLASE/OXYGENASE
W: RIBULOSE BISPHOSPHATE CARBOXYLASE/OXYGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)541,61224
Polymers538,98716
Non-polymers2,6258
Water34,3011904
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area109990 Å2
ΔGint-516 kcal/mol
Surface area119700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)220.600, 221.700, 115.300
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.968469, 0.213962, 0.127625), (0.213521, -0.976785, 0.01729), (0.128362, 0.010506, -0.991672)-15.4124, 105.5144, 60.9497
2given(0.000353, -0.994401, -0.105676), (0.999919, -0.000993, 0.012685), (-0.012719, -0.105672, 0.99432)-0.0842, 98.594, 4.5653
3given(-0.222218, 0.970791, 0.090465), (0.97053, 0.211374, 0.115725), (0.093222, 0.113516, -0.989153)-111.3166, 84.0224, 54.0894
4given(-0.993249, 0.005479, -0.115873), (0.005799, -0.99529, -0.096765), (-0.115858, -0.096784, 0.988539)-98.3414, 99.0034, -0.9606
5given(-0.975992, -0.217612, -0.009175), (-0.217656, 0.972892, 0.078143), (-0.008079, 0.078264, -0.9969)-89.6653, -11.9117, 50.7982
6given(0.003663, 0.999973, -0.006347), (-0.993949, 0.002944, -0.1098), (-0.109778, 0.006711, 0.993933)-98.4566, 0.5645, -5.7965
7given(0.216926, -0.975745, 0.029423), (-0.975965, -0.217422, -0.014844), (0.020881, -0.025496, -0.999457)6.4796, 9.5179, 57.3717
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.: 8 / 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.: 8 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / Organ: LEAF
References: UniProt: P00870, ribulose-bisphosphate carboxylase
#3: Sugar
ChemComp-XDP / D-XYLULOSE-2,2-DIOL-1,5-BISPHOSPHATE


Type: D-saccharide / Mass: 328.105 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Formula: C5H14O12P2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1904 / 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: 11

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Sample preparation

CrystalDensity Matthews: 2.61 Å3/Da / Density % sol: 40 %
Crystal growpH: 7.8
Details: 15% PEG 4000, 25 MM HEPES PH 7.8, 10 MM CACL2, 0.2 M NACL, 50 MM NAHCO3, 20 MM XUBP
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
160 mg/mlprotein1drop
225 mMHEPES1drop
310 mM1dropCaCl2
450 mM1dropNaHCO3
520 mMXuBP1drop
615-16 %PEG40001reservoir
725 mMHEPES1reservoir
80.2 M1reservoirNaCl
950 mM1reservoirNaHCO3

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Data collection

DiffractionMean temperature: 279 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.5
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 1, 1990
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.3→20 Å / Num. obs: 217862 / % possible obs: 62.5 % / Redundancy: 7 % / Rmerge(I) obs: 0.147 / Net I/σ(I): 3.4
Reflection shellResolution: 2.3→2.36 Å / Redundancy: 1.3 % / Rmerge(I) obs: 0.413 / Mean I/σ(I) obs: 1.3 / % possible all: 62.5
Reflection
*PLUS
Num. measured all: 1519008
Reflection shell
*PLUS
% possible obs: 62.5 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.1model building
X-PLOR3.1refinement
X-PLOR3.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 8RUC

8ruc


Resolution: 2.3→7 Å / Isotropic thermal model: INDIVIDUAL / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.246 10679 5 %RANDOM
Rwork0.239 ---
obs0.239 205853 63 %-
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-4.94 Å20 Å20 Å2
2---1.34 Å20 Å2
3----3.6 Å2
Refinement stepCycle: LAST / Resolution: 2.3→7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4682 0 19 238 4939
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.016
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_deg1.822
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24.1
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.46
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
Rfree0.341 963 5 %
Rwork0.342 18380 -
obs--64.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2WAT.PARAWAT.TOP
X-RAY DIFFRACTION3XUBP_DIOL.PARAXUBP_DIOL.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_deg24.1
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.46
LS refinement shell
*PLUS
Rfactor obs: 0.342

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