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- PDB-6kyj: Hybrid-Rubisco (rice RbcL and sorghum RbcS) in complex with sulfa... -

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Basic information

Entry
Database: PDB / ID: 6kyj
TitleHybrid-Rubisco (rice RbcL and sorghum RbcS) in complex with sulfate ions
Components
  • Ribulose bisphosphate carboxylase large chain
  • Ribulose bisphosphate carboxylase small chain
KeywordsPHOTOSYNTHESIS / CO2 assimilation / C4 plant / rice / Rubisco
Function / homology
Function and homology information


photorespiration / ribulose-bisphosphate carboxylase / ribulose-bisphosphate carboxylase activity / reductive pentose-phosphate cycle / plastid / chloroplast / monooxygenase activity / magnesium ion binding
Similarity search - Function
Ribulose-1,5-bisphosphate carboxylase small subunit, N-terminal / Ribulose-1,5-bisphosphate carboxylase small subunit / 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-1,5-bisphosphate carboxylase small subunit, N-terminal / Ribulose-1,5-bisphosphate carboxylase small subunit / 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
Ribulose bisphosphate carboxylase small subunit, chloroplastic / Ribulose bisphosphate carboxylase large chain
Similarity search - Component
Biological speciesOryza sativa (Asian cultivated rice)
Sorghum bicolor (sorghum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsMatsumura, H. / Yoshizawa, T. / Tanaka, S. / Yoshikawa, H.
Funding support Japan, 4items
OrganizationGrant numberCountry
Ministry of Education, Culture, Sports, Science and Technology (Japan)19K07582 Japan
Ministry of Education, Culture, Sports, Science and Technology (Japan)19H04735 Japan
Ministry of Education, Culture, Sports, Science and Technology (Japan)18K06094 Japan
Ministry of Education, Culture, Sports, Science and Technology (Japan)17H05732 Japan
CitationJournal: Mol Plant / Year: 2020
Title: Hybrid Rubisco with Complete Replacement of Rice Rubisco Small Subunits by Sorghum Counterparts Confers C 4 Plant-like High Catalytic Activity.
Authors: Matsumura, H. / Shiomi, K. / Yamamoto, A. / Taketani, Y. / Kobayashi, N. / Yoshizawa, T. / Tanaka, S.I. / Yoshikawa, H. / Endo, M. / Fukayama, H.
History
DepositionSep 19, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 16, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 18, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ribulose bisphosphate carboxylase large chain
S: Ribulose bisphosphate carboxylase small chain
E: Ribulose bisphosphate carboxylase large chain
W: Ribulose bisphosphate carboxylase small chain
C: Ribulose bisphosphate carboxylase large chain
U: Ribulose bisphosphate carboxylase small chain
G: Ribulose bisphosphate carboxylase large chain
Y: Ribulose bisphosphate carboxylase small chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)291,45842
Polymers288,2438
Non-polymers3,21534
Water24,0501335
1
A: Ribulose bisphosphate carboxylase large chain
S: Ribulose bisphosphate carboxylase small chain
hetero molecules

A: Ribulose bisphosphate carboxylase large chain
S: Ribulose bisphosphate carboxylase small chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)145,82722
Polymers144,1224
Non-polymers1,70518
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area14460 Å2
ΔGint-70 kcal/mol
Surface area39390 Å2
MethodPISA
2
E: Ribulose bisphosphate carboxylase large chain
W: Ribulose bisphosphate carboxylase small chain
hetero molecules

G: Ribulose bisphosphate carboxylase large chain
Y: Ribulose bisphosphate carboxylase small chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)145,72721
Polymers144,1224
Non-polymers1,60517
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area14450 Å2
ΔGint-68 kcal/mol
Surface area40070 Å2
MethodPISA
3
C: Ribulose bisphosphate carboxylase large chain
U: Ribulose bisphosphate carboxylase small chain
hetero molecules

C: Ribulose bisphosphate carboxylase large chain
U: Ribulose bisphosphate carboxylase small chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)145,63520
Polymers144,1224
Non-polymers1,51316
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area14510 Å2
ΔGint-69 kcal/mol
Surface area39870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)223.790, 223.790, 108.940
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number90
Space group name H-MP4212
Space group name HallP4ab2ab
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z
#3: y+1/2,-x+1/2,z
#4: x+1/2,-y+1/2,-z
#5: -x+1/2,y+1/2,-z
#6: -x,-y,z
#7: y,x,-z
#8: -y,-x,-z
Components on special symmetry positions
IDModelComponents
11A-678-

HOH

21A-758-

HOH

31A-820-

HOH

41A-831-

HOH

51C-717-

HOH

61C-722-

HOH

71C-806-

HOH

81C-810-

HOH

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Components

#1: Protein
Ribulose bisphosphate carboxylase large chain / RuBisCO large subunit


Mass: 52950.027 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryza sativa (Asian cultivated rice) / Gene: rbcL, PA064 / Production host: Escherichia coli (E. coli)
References: UniProt: P0C510, ribulose-bisphosphate carboxylase
#2: Protein
Ribulose bisphosphate carboxylase small chain


Mass: 19110.840 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sorghum bicolor (sorghum) / Gene: RbcS / Production host: Escherichia coli (E. coli)
References: UniProt: E3WDK7, ribulose-bisphosphate carboxylase
#3: Chemical...
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 21 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 13 / Source method: isolated from a natural source / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1335 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.37 Å3/Da / Density % sol: 48.01 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.1M Tris-HCl (pH 9.0), 0.2M lithium sulfate, 15%(w/v) polyethylene glycol 4000, and 10 %(w/v) glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Oct 18, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→48.58 Å / Num. obs: 299765 / % possible obs: 99.98 % / Redundancy: 27.2 % / Biso Wilson estimate: 20.19 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.1184 / Rpim(I) all: 0.02303 / Rrim(I) all: 0.1207 / Net I/σ(I): 23.31
Reflection shellResolution: 1.7→1.761 Å / Rmerge(I) obs: 1.138 / Mean I/σ(I) obs: 3.13 / Num. unique obs: 29707 / CC1/2: 0.82 / Rpim(I) all: 0.2335

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3AXM

3axm


Resolution: 1.7→48.58 Å / SU ML: 0.1591 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 17.1838
RfactorNum. reflection% reflection
Rfree0.1847 14987 5 %
Rwork0.1624 --
obs0.1635 299744 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 22.26 Å2
Refinement stepCycle: LAST / Resolution: 1.7→48.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17974 0 183 1335 19492
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006718822
X-RAY DIFFRACTIONf_angle_d0.851725548
X-RAY DIFFRACTIONf_chiral_restr0.05212677
X-RAY DIFFRACTIONf_plane_restr0.00563303
X-RAY DIFFRACTIONf_dihedral_angle_d2.920715956
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.720.26264930.22969368X-RAY DIFFRACTION100
1.72-1.740.2634970.21799430X-RAY DIFFRACTION100
1.74-1.760.22594960.20949423X-RAY DIFFRACTION100
1.76-1.780.21654930.19019375X-RAY DIFFRACTION100
1.78-1.810.23064950.18739408X-RAY DIFFRACTION100
1.81-1.830.22084950.18669408X-RAY DIFFRACTION100
1.83-1.860.22494970.18569440X-RAY DIFFRACTION99.99
1.86-1.890.21474950.18199396X-RAY DIFFRACTION100
1.89-1.910.21594970.17499445X-RAY DIFFRACTION99.99
1.91-1.950.21044960.17739422X-RAY DIFFRACTION100
1.95-1.980.20634950.16959416X-RAY DIFFRACTION99.99
1.98-2.020.20774960.16829422X-RAY DIFFRACTION100
2.02-2.050.20774980.17229448X-RAY DIFFRACTION100
2.05-2.10.20684960.17039435X-RAY DIFFRACTION100
2.1-2.140.19124970.16459439X-RAY DIFFRACTION100
2.14-2.190.21524960.16849414X-RAY DIFFRACTION99.99
2.19-2.250.18114990.15879495X-RAY DIFFRACTION100
2.25-2.310.20384980.1639458X-RAY DIFFRACTION100
2.31-2.380.1954980.15889459X-RAY DIFFRACTION99.96
2.38-2.450.18934980.1619463X-RAY DIFFRACTION100
2.45-2.540.18675020.16249526X-RAY DIFFRACTION99.98
2.54-2.640.19844980.16529465X-RAY DIFFRACTION100
2.64-2.760.18225000.16459501X-RAY DIFFRACTION100
2.76-2.910.19945010.16789533X-RAY DIFFRACTION100
2.91-3.090.17235020.1649523X-RAY DIFFRACTION100
3.09-3.330.18885040.16349590X-RAY DIFFRACTION100
3.33-3.660.16835060.15899605X-RAY DIFFRACTION100
3.66-4.190.15185070.13439643X-RAY DIFFRACTION99.99
4.19-5.280.1435120.13519728X-RAY DIFFRACTION99.99
5.28-48.580.16455300.166810079X-RAY DIFFRACTION99.88

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