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- PDB-1rxo: ACTIVATED SPINACH RUBISCO IN COMPLEX WITH ITS SUBSTRATE RIBULOSE-... -

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Basic information

Entry
Database: PDB / ID: 1rxo
TitleACTIVATED SPINACH RUBISCO IN COMPLEX WITH ITS SUBSTRATE RIBULOSE-1,5-BISPHOSPHATE AND CALCIUM
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 / 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
RIBULOSE-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 PDB ENTRY 1AUS / Resolution: 2.2 Å
AuthorsTaylor, T.C. / Andersson, I.
Citation
Journal: J.Mol.Biol. / Year: 1997
Title: The structure of the complex between rubisco and its natural substrate ribulose 1,5-bisphosphate.
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
DepositionDec 6, 1996-
Revision 1.0Jun 16, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)271,06616
Polymers269,6658
Non-polymers1,4018
Water18,4471024
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)542,13232
Polymers539,33116
Non-polymers2,80116
Water28816
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area102440 Å2
ΔGint-508 kcal/mol
Surface area121500 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)157.600, 158.500, 202.600
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(0.000861, 0.999995, 0.003146), (-0.999999, 0.000864, -0.001116), (-0.001119, -0.003145, 0.999994)-37.7925, 37.5427, 0.065
2given(-0.999964, -7.8E-5, 0.008451), (8.1E-5, -1, 0.000409), (0.008451, 0.00041, 0.999964)-0.4383, 75.2254, -0.0021
3given(-0.001308, -0.999988, 0.004751), (0.999998, -0.001315, -0.00142), (0.001426, 0.004749, 0.999988)37.3432, 37.816, -0.2139
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: 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/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-RUB / RIBULOSE-1,5-DIPHOSPHATE / Ribulose 1,5-bisphosphate


Type: saccharideCarbohydrate / Mass: 310.090 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C5H12O11P2
#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1024 / 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: 4

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Sample preparation

CrystalDensity Matthews: 2.34 Å3/Da / Density % sol: 40 %
Crystal growpH: 7.8
Details: 14% PEG4000, 25 MM HEPES PH 7.8, 0.2 M NACL, 10 MM CACL2; SOAKED WITH 20 MM RUBP FOR 5 DAYS
Crystal
*PLUS
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
110 mM1dropMgCl2
250 mM1dropNaHCO3
35 mMHEPES1drop
40.02 %1dropNaN3
550-60 mg/mlprotain1drop
6100 mM3-PGA1drop
714-16 %PEG40001reservoir
80.2 M1reservoirNaCl
925 mMHEPES1reservoir
1010 mM1reservoirMgCl2
1150 mM1reservoirNaHCO3
120.02 %1reservoirNaN3

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Data collection

DiffractionMean temperature: 279 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 1, 1994
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 2.1→20 Å / Num. obs: 109900 / % possible obs: 75.5 % / Redundancy: 6 % / Rmerge(I) obs: 0.136 / Net I/σ(I): 6.9
Reflection shellResolution: 2.1→2.17 Å / Redundancy: 2 % / Rmerge(I) obs: 0.247 / Mean I/σ(I) obs: 2.8 / % possible all: 53.8
Reflection
*PLUS
Num. measured all: 1275669

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.1phasing
RefinementMethod to determine structure: ISOMORPHOUS WITH PDB ENTRY 1AUS
Resolution: 2.2→7 Å / Isotropic thermal model: INDIVIDUAL / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.229 5667 5 %RANDOM
Rwork0.205 ---
obs0.205 108984 88 %-
Refinement stepCycle: LAST / Resolution: 2.2→7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18340 0 76 1024 19440
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.011
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_deg1.947
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d23
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.44
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
Rfree0.27 625 5 %
Rwork0.243 11331 -
obs--77.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2WAT.PARAWAT.TOP
X-RAY DIFFRACTION3RUBP.PARARUBP.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_deg23
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.44
LS refinement shell
*PLUS
Rfactor Rfree: 0.27

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