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- PDB-3axk: Structure of rice Rubisco in complex with NADP(H) -

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Basic information

Entry
Database: PDB / ID: 3axk
TitleStructure of rice Rubisco in complex with NADP(H)
Components(Ribulose bisphosphate carboxylase ...) x 2
KeywordsLYASE / alpha/beta barrel / photosynthetic carbon reduction
Function / homology
Function and homology information


photorespiration / ribulose-bisphosphate carboxylase / ribulose-bisphosphate carboxylase activity / reductive pentose-phosphate cycle / plastid / monooxygenase activity / chloroplast / nucleotide binding / 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
Chem-NDP / Ribulose bisphosphate carboxylase large chain / Ribulose bisphosphate carboxylase small subunit, chloroplastic 1
Similarity search - Component
Biological speciesOryza sativa Japonica Group (Japanese rice)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsMatsumura, H. / Mizohata, E. / Ishida, H. / Kogami, A. / Ueno, T. / Makino, A. / Inoue, T. / Yokota, A. / Mae, T. / Kai, Y.
CitationJournal: J.Mol.Biol. / Year: 2012
Title: Crystal structure of rice Rubisco and implications for activation induced by positive effectors NADPH and 6-phosphogluconate
Authors: Matsumura, H. / Mizohata, E. / Ishida, H. / Kogami, A. / Ueno, T. / Makino, A. / Inoue, T. / Yokota, A. / Mae, T. / Kai, Y.
History
DepositionApr 11, 2011Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 11, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 13, 2012Group: Database references
Revision 1.2Jun 5, 2013Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ribulose bisphosphate carboxylase large chain
S: Ribulose bisphosphate carboxylase small chain, chloroplastic
B: Ribulose bisphosphate carboxylase large chain
T: Ribulose bisphosphate carboxylase small chain, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)137,83312
Polymers135,9254
Non-polymers1,9088
Water20,2671125
1
A: Ribulose bisphosphate carboxylase large chain
S: Ribulose bisphosphate carboxylase small chain, chloroplastic
B: Ribulose bisphosphate carboxylase large chain
T: Ribulose bisphosphate carboxylase small chain, chloroplastic
hetero molecules

A: Ribulose bisphosphate carboxylase large chain
S: Ribulose bisphosphate carboxylase small chain, chloroplastic
B: Ribulose bisphosphate carboxylase large chain
T: Ribulose bisphosphate carboxylase small chain, chloroplastic
hetero molecules

A: Ribulose bisphosphate carboxylase large chain
S: Ribulose bisphosphate carboxylase small chain, chloroplastic
B: Ribulose bisphosphate carboxylase large chain
T: Ribulose bisphosphate carboxylase small chain, chloroplastic
hetero molecules

A: Ribulose bisphosphate carboxylase large chain
S: Ribulose bisphosphate carboxylase small chain, chloroplastic
B: Ribulose bisphosphate carboxylase large chain
T: Ribulose bisphosphate carboxylase small chain, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)551,33048
Polymers543,69916
Non-polymers7,63132
Water28816
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation3_655-y+1,x,z1
crystal symmetry operation4_565y,-x+1,z1
Buried area91580 Å2
ΔGint-356 kcal/mol
Surface area118410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.246, 110.246, 199.768
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4

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Components

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Ribulose bisphosphate carboxylase ... , 2 types, 4 molecules ABST

#1: Protein Ribulose bisphosphate carboxylase large chain / RuBisCO large subunit / D-Ribulose 1 / 5-bisphosphate carboxylase/oxygenase large subunit


Mass: 52993.031 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Oryza sativa Japonica Group (Japanese rice)
Tissue: leaves
References: UniProt: P0C512, ribulose-bisphosphate carboxylase
#2: Protein Ribulose bisphosphate carboxylase small chain, chloroplastic / RuBisCO small subunit / D-Ribulose 1 / 5-bisphosphate carboxylase/oxygenase small subunit


Mass: 14969.305 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Oryza sativa Japonica Group (Japanese rice)
Tissue: leaves
References: UniProt: Q0INY7, ribulose-bisphosphate carboxylase

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Non-polymers , 4 types, 1133 molecules

#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1125 / 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: 1

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Sample preparation

CrystalDensity Matthews: 2.23 Å3/Da / Density % sol: 44.91 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 8
Details: 75mM HEPES-KOH (pH 7.75), 9% PEG4000, 25% glycerol, VAPOR DIFFUSION, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU ULTRAX 18 / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Nov 1, 2003
RadiationMonochromator: YALE MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.9→39.63 Å / Num. obs: 89311 / Observed criterion σ(F): 10.5 / Observed criterion σ(I): 10.5 / Biso Wilson estimate: 13.8 Å2 / Rmerge(I) obs: 0.07

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Processing

Software
NameClassification
HKL-2000data collection
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→39.63 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 369893.34 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.189 3848 4.3 %RANDOM
Rwork0.169 ---
obs0.169 88564 94.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 67.0296 Å2 / ksol: 0.367278 e/Å3
Displacement parametersBiso mean: 20.4 Å2
Baniso -1Baniso -2Baniso -3
1-0.53 Å20 Å20 Å2
2--0.53 Å20 Å2
3----1.07 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.2 Å0.17 Å
Luzzati d res low-5 Å
Luzzati sigma a0.14 Å0.13 Å
Refinement stepCycle: LAST / Resolution: 1.9→39.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8745 0 122 1125 9992
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d23
X-RAY DIFFRACTIONc_improper_angle_d0.79
X-RAY DIFFRACTIONc_mcbond_it1.241.5
X-RAY DIFFRACTIONc_mcangle_it1.852
X-RAY DIFFRACTIONc_scbond_it1.892
X-RAY DIFFRACTIONc_scangle_it2.632.5
LS refinement shellResolution: 1.9→2.02 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.213 103 0.7 %
Rwork0.197 13812 -
obs--90.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top
X-RAY DIFFRACTION4rub.paramrub.top

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