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- PDB-6ius: A higher kcat Rubisco -

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Basic information

Entry
Database: PDB / ID: 6ius
TitleA higher kcat Rubisco
ComponentsRibulose-1,5-bisphosphate carboxylase/oxygenase
KeywordsBIOSYNTHETIC PROTEIN
Function / homology
Function and homology information


ribulose-bisphosphate carboxylase / carbon fixation / ribulose-bisphosphate carboxylase activity / magnesium ion binding
Similarity search - Function
Ribulose bisphosphate carboxylase large subunit, type II / Ribulose bisphosphate carboxylase, large subunit, C-terminal domain / RuBisCO large subunit, N-terminal domain / 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 ...Ribulose bisphosphate carboxylase large subunit, type II / Ribulose bisphosphate carboxylase, large subunit, C-terminal domain / RuBisCO large subunit, N-terminal domain / 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
Similarity search - Component
Biological speciesendosymbiont of Riftia pachyptila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.12 Å
AuthorsLi, Y. / Cai, Z.
CitationJournal: To Be Published
Title: A higher kcat Rubisco
Authors: Li, Y. / Cai, Z.
History
DepositionNov 30, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 4, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ribulose-1,5-bisphosphate carboxylase/oxygenase
B: Ribulose-1,5-bisphosphate carboxylase/oxygenase
C: Ribulose-1,5-bisphosphate carboxylase/oxygenase


Theoretical massNumber of molelcules
Total (without water)151,9773
Polymers151,9773
Non-polymers00
Water12,719706
1
A: Ribulose-1,5-bisphosphate carboxylase/oxygenase
C: Ribulose-1,5-bisphosphate carboxylase/oxygenase


Theoretical massNumber of molelcules
Total (without water)101,3182
Polymers101,3182
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5810 Å2
ΔGint-28 kcal/mol
Surface area29410 Å2
MethodPISA
2
B: Ribulose-1,5-bisphosphate carboxylase/oxygenase

B: Ribulose-1,5-bisphosphate carboxylase/oxygenase


Theoretical massNumber of molelcules
Total (without water)101,3182
Polymers101,3182
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area5730 Å2
ΔGint-30 kcal/mol
Surface area29020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)166.501, 107.842, 112.306
Angle α, β, γ (deg.)90.00, 130.04, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-714-

HOH

21B-600-

HOH

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Components

#1: Protein Ribulose-1,5-bisphosphate carboxylase/oxygenase


Mass: 50659.105 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) endosymbiont of Riftia pachyptila (bacteria)
Gene: cbbM / Production host: Escherichia coli (E. coli) / References: UniProt: O68486
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 706 / 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: 2.54 Å3/Da / Density % sol: 51.57 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 0.15M Magnesium formate, 12%(w/v) Polyethylene glycol 3,350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 11, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.12→50 Å / Num. obs: 86160 / % possible obs: 99.8 % / Redundancy: 6.8 % / Rmerge(I) obs: 0.138 / Rpim(I) all: 0.056 / Net I/σ(I): 25.4
Reflection shellResolution: 2.12→2.16 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.396 / Mean I/σ(I) obs: 3.4 / Rpim(I) all: 0.166 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
HKL-3000data reduction
HKL-3000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5C2C

5c2c


Resolution: 2.12→46.99 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.929 / SU B: 5.039 / SU ML: 0.131 / Cross valid method: THROUGHOUT / ESU R: 0.218 / ESU R Free: 0.181 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23074 1926 2.3 %RANDOM
Rwork0.1923 ---
obs0.19319 80964 96.06 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 38.601 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å2-0 Å2-0.01 Å2
2--0 Å2-0 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 2.12→46.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9798 0 0 706 10504
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.01310096
X-RAY DIFFRACTIONr_bond_other_d0.0010.0179159
X-RAY DIFFRACTIONr_angle_refined_deg1.6471.64813657
X-RAY DIFFRACTIONr_angle_other_deg1.3531.58121246
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.52551260
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.65522.49526
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.373151584
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.9681555
X-RAY DIFFRACTIONr_chiral_restr0.080.21283
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0211475
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022190
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.383.9745064
X-RAY DIFFRACTIONr_mcbond_other3.383.9735063
X-RAY DIFFRACTIONr_mcangle_it4.7165.9416316
X-RAY DIFFRACTIONr_mcangle_other4.7165.9426317
X-RAY DIFFRACTIONr_scbond_it3.6984.2685030
X-RAY DIFFRACTIONr_scbond_other3.6984.2685031
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.376.2687339
X-RAY DIFFRACTIONr_long_range_B_refined7.15847.61611737
X-RAY DIFFRACTIONr_long_range_B_other7.15847.61911738
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.118→2.173 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.262 135 -
Rwork0.213 5561 -
obs--89.9 %

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