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- PDB-6kyi: Rice Rubisco in complex with sulfate ions -

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Basic information

Entry
Database: PDB / ID: 6kyi
TitleRice Rubisco in complex with sulfate ions
Components
  • Ribulose bisphosphate carboxylase large chain
  • Ribulose bisphosphate carboxylase small chain, chloroplastic
KeywordsPHOTOSYNTHESIS / CO2 assimilation / 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 / 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-1,5-bisphosphate carboxylase small subunit, N-terminal / Ribulose-1,5-bisphosphate carboxylase small subunit / 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 / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Ribulose bisphosphate carboxylase large chain / Ribulose bisphosphate carboxylase small subunit, chloroplastic 1
Similarity search - Component
Biological speciesOryza sativa (Asian cultivated rice)
Oryza sativa subsp. japonica (Japanese rice)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 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 1.3Oct 23, 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

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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)145,90211
Polymers145,2374
Non-polymers6657
Water15,187843
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)583,60844
Polymers580,95016
Non-polymers2,65828
Water28816
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
Buried area99350 Å2
ΔGint-661 kcal/mol
Surface area117770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.061, 110.061, 199.748
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number79
Space group name H-MI4
Space group name HallI4
Symmetry operation#1: x,y,z
#2: -y,x,z
#3: y,-x,z
#4: -x,-y,z
#5: x+1/2,y+1/2,z+1/2
#6: -y+1/2,x+1/2,z+1/2
#7: y+1/2,-x+1/2,z+1/2
#8: -x+1/2,-y+1/2,z+1/2

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Components

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


Mass: 52950.027 Da / Num. of mol.: 2
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, chloroplastic / RuBisCO small subunit C


Mass: 19668.662 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryza sativa subsp. japonica (Japanese rice)
Gene: RBCS, RBCS-C, Os12g0274700, LOC_Os12g17600, OsJ_016909, OsJ_17688
Production host: Escherichia coli (E. coli)
References: UniProt: Q0INY7, ribulose-bisphosphate carboxylase
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / 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.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 843 / 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: 2.08 Å3/Da / Density % sol: 40.94 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.1 M Tris-HCl (pH 9.0), 0.2 M 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: Jan 30, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.75→42.03 Å / Num. obs: 118922 / % possible obs: 99.91 % / Redundancy: 14.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.104 / Rpim(I) all: 0.0278 / Rrim(I) all: 0.107 / Net I/σ(I): 23.31
Reflection shellResolution: 1.75→1.813 Å / Redundancy: 11.7 % / Rmerge(I) obs: 0.8866 / Mean I/σ(I) obs: 2.85 / Num. unique obs: 11805 / CC1/2: 0.721 / Rpim(I) all: 0.2663 / Rrim(I) all: 0.927 / % possible all: 99.26

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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: 1.75→42.03 Å / Cross valid method: THROUGHOUT / σ(F): 66.49 / Phase error: 14.523
RfactorNum. reflection% reflection
Rfree0.1433 5948 5 %
Rwork0.129 --
obs0.1369 118917 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 19.43 Å2
Refinement stepCycle: LAST / Resolution: 1.75→42.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8801 0 37 843 9681
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00299124
X-RAY DIFFRACTIONf_angle_d0.600812377
X-RAY DIFFRACTIONf_chiral_restr0.04291309
X-RAY DIFFRACTIONf_plane_restr0.00391601
X-RAY DIFFRACTIONf_dihedral_angle_d2.6417716
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.780.22572930.22465558X-RAY DIFFRACTION93.73
1.78-1.810.22172980.19775654X-RAY DIFFRACTION94.85
1.81-1.850.19332940.18525596X-RAY DIFFRACTION94.99
1.85-1.890.19532980.17465663X-RAY DIFFRACTION94.97
1.89-1.930.17812970.16495647X-RAY DIFFRACTION95
1.93-1.970.17012970.15685635X-RAY DIFFRACTION94.99
1.97-2.020.15042960.15385622X-RAY DIFFRACTION95
2.02-2.070.17763000.15385699X-RAY DIFFRACTION94.98
2.07-2.140.16912950.14975612X-RAY DIFFRACTION95.01
2.14-2.20.16062980.14355651X-RAY DIFFRACTION94.99
2.2-2.280.15252960.14475631X-RAY DIFFRACTION95.01
2.28-2.380.14472970.1365640X-RAY DIFFRACTION95
2.38-2.480.16082980.13725674X-RAY DIFFRACTION95.01
2.48-2.610.15212970.13725644X-RAY DIFFRACTION95
2.61-2.780.14922980.12885654X-RAY DIFFRACTION94.99
2.78-2.990.14272970.12915651X-RAY DIFFRACTION95.01
2.99-3.290.14322990.12525664X-RAY DIFFRACTION94.99
3.29-3.770.13372970.11635661X-RAY DIFFRACTION95.02
3.77-4.750.11512990.10725668X-RAY DIFFRACTION94.99
4.75-39.590.14713020.13735732X-RAY DIFFRACTION94.98

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