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- PDB-8bdb: Ribulose-1,5-bisphosphate carboxylase/oxygenase from Griffithsia ... -

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Basic information

Entry
Database: PDB / ID: 8bdb
TitleRibulose-1,5-bisphosphate carboxylase/oxygenase from Griffithsia monilis
Components
  • (Ribulose bisphosphate carboxylase large ...) x 2
  • Ribulose bisphosphate carboxylase small chain
KeywordsPHOTOSYNTHESIS / carbon dioxide fixation / photorespiration / lyase (carbon-carbon)
Function / homology
Function and homology information


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 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, 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
Similarity search - Domain/homology
BICARBONATE ION / 2-CARBOXYARABINITOL-1,5-DIPHOSPHATE / Ribulose bisphosphate carboxylase large chain / Multifunctional fusion protein
Similarity search - Component
Biological speciesGriffithsia monilis (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsAndersson, I. / Gunn, L.H.
Funding support Sweden, 1items
OrganizationGrant numberCountry
Swedish Research Council2015-05007 Sweden
CitationJournal: Nat.Plants / Year: 2023
Title: Grafting Rhodobacter sphaeroides with red algae Rubisco to accelerate catalysis and plant growth.
Authors: Zhou, Y. / Gunn, L.H. / Birch, R. / Andersson, I. / Whitney, S.M.
History
DepositionOct 19, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 14, 2023Provider: repository / Type: Initial release
Revision 1.1Jun 21, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Jun 28, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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
B: Ribulose bisphosphate carboxylase small chain
C: Ribulose bisphosphate carboxylase large chain
D: Ribulose bisphosphate carboxylase small chain
E: Ribulose bisphosphate carboxylase large chain
F: Ribulose bisphosphate carboxylase small chain
G: Ribulose bisphosphate carboxylase large chain
H: Ribulose bisphosphate carboxylase small chain
I: Ribulose bisphosphate carboxylase large chain
J: Ribulose bisphosphate carboxylase small chain
K: Ribulose bisphosphate carboxylase large chain
L: Ribulose bisphosphate carboxylase small chain
M: Ribulose bisphosphate carboxylase large chain
N: Ribulose bisphosphate carboxylase small chain
O: Ribulose bisphosphate carboxylase large chain
P: Ribulose bisphosphate carboxylase small chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)571,319196
Polymers558,12916
Non-polymers13,190180
Water57,5403194
1
A: Ribulose bisphosphate carboxylase large chain
B: Ribulose bisphosphate carboxylase small chain
C: Ribulose bisphosphate carboxylase large chain
D: Ribulose bisphosphate carboxylase small chain
M: Ribulose bisphosphate carboxylase large chain
N: Ribulose bisphosphate carboxylase small chain
O: Ribulose bisphosphate carboxylase large chain
P: Ribulose bisphosphate carboxylase small chain
hetero molecules

A: Ribulose bisphosphate carboxylase large chain
B: Ribulose bisphosphate carboxylase small chain
C: Ribulose bisphosphate carboxylase large chain
D: Ribulose bisphosphate carboxylase small chain
M: Ribulose bisphosphate carboxylase large chain
N: Ribulose bisphosphate carboxylase small chain
O: Ribulose bisphosphate carboxylase large chain
P: Ribulose bisphosphate carboxylase small chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)571,378196
Polymers558,18716
Non-polymers13,191180
Water28816
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_554-x,y,-z-11
2
E: Ribulose bisphosphate carboxylase large chain
F: Ribulose bisphosphate carboxylase small chain
G: Ribulose bisphosphate carboxylase large chain
H: Ribulose bisphosphate carboxylase small chain
I: Ribulose bisphosphate carboxylase large chain
J: Ribulose bisphosphate carboxylase small chain
K: Ribulose bisphosphate carboxylase large chain
L: Ribulose bisphosphate carboxylase small chain
hetero molecules

E: Ribulose bisphosphate carboxylase large chain
F: Ribulose bisphosphate carboxylase small chain
G: Ribulose bisphosphate carboxylase large chain
H: Ribulose bisphosphate carboxylase small chain
I: Ribulose bisphosphate carboxylase large chain
J: Ribulose bisphosphate carboxylase small chain
K: Ribulose bisphosphate carboxylase large chain
L: Ribulose bisphosphate carboxylase small chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)571,260196
Polymers558,07116
Non-polymers13,189180
Water28816
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Unit cell
Length a, b, c (Å)210.328, 131.925, 196.319
Angle α, β, γ (deg.)90.000, 94.750, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-612-

HOH

21E-702-

HOH

31E-881-

HOH

41G-899-

HOH

51M-878-

HOH

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Components

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Ribulose bisphosphate carboxylase large ... , 2 types, 8 molecules ACGKOEIM

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


Mass: 53616.914 Da / Num. of mol.: 5 / Source method: isolated from a natural source
Details: ribulose-1,5-bisphosphate carboxylase/oxygenase rbcL
Source: (natural) Griffithsia monilis (eukaryote)
References: UniProt: A7UM67, ribulose-bisphosphate carboxylase
#3: Protein Ribulose bisphosphate carboxylase large chain / RuBisCO large subunit / Ribulose-1 / 5-bisphosphate carboxylase/oxygenase rbcL


Mass: 53558.875 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Griffithsia monilis (eukaryote)
References: UniProt: A7UM67, ribulose-bisphosphate carboxylase

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Protein / Sugars , 2 types, 16 molecules BDFHJLNP

#2: Protein
Ribulose bisphosphate carboxylase small chain / Multifunctional fusion protein / Ribulose-1 / 5-bisphosphate carboxylase/oxygenase rbcS


Mass: 16170.936 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Source: (natural) Griffithsia monilis (eukaryote) / References: UniProt: A7UM68
#5: Sugar
ChemComp-CAP / 2-CARBOXYARABINITOL-1,5-DIPHOSPHATE


Type: saccharideCarbohydrate / Mass: 356.115 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C6H14O13P2

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Non-polymers , 4 types, 3366 molecules

#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg
#6: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 133 / Source method: obtained synthetically / Formula: C2H6O2
#7: Chemical...
ChemComp-BCT / BICARBONATE ION / Bicarbonate


Mass: 61.017 Da / Num. of mol.: 31 / Source method: obtained synthetically / Formula: CHO3 / Feature type: SUBJECT OF INVESTIGATION / Comment: pH buffer*YM
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 3194 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.41 Å3/Da / Density % sol: 49.1 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: HEPES, lithium sulphate, PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 15, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.7→49.6 Å / Num. obs: 578867 / % possible obs: 99.2 % / Redundancy: 3.3 % / Biso Wilson estimate: 16.2 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.101 / Rpim(I) all: 0.095 / Rrim(I) all: 0.139 / Net I/σ(I): 7.6
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.891 / Mean I/σ(I) obs: 0.9 / Num. unique obs: 25785 / CC1/2: 0.36 / Rpim(I) all: 0.857 / Rrim(I) all: 1.238 / % possible all: 89.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0107refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1BWV

1bwv


Resolution: 1.7→49.6 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.961 / SU B: 2.399 / SU ML: 0.072 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.093 / ESU R Free: 0.087 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.178 1980 5 %RANDOM
Rwork0.1578 ---
obs0.1588 549779 99.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 72.13 Å2 / Biso mean: 18.2 Å2 / Biso min: 8.25 Å2
Baniso -1Baniso -2Baniso -3
1--0.69 Å20 Å20.29 Å2
2--0.16 Å20 Å2
3---0.48 Å2
Refinement stepCycle: final / Resolution: 1.7→49.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms39120 0 832 3194 43146
Biso mean--28.6 24.84 -
Num. residues----4926
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01941109
X-RAY DIFFRACTIONr_bond_other_d0.0020.0238862
X-RAY DIFFRACTIONr_angle_refined_deg1.2761.95955487
X-RAY DIFFRACTIONr_angle_other_deg0.909389166
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.55754910
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.00623.7981967
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.264156758
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.36415286
X-RAY DIFFRACTIONr_chiral_restr0.0750.26021
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02146168
X-RAY DIFFRACTIONr_gen_planes_other0.0020.029730
LS refinement shellResolution: 1.701→1.745 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.311 1963 -
Rwork0.305 37361 -
all-39324 -
obs--91.47 %

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