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- PDB-7t1j: Crystal structure of RUBISCO from Rhodospirillaceae bacterium BRH_c57 -

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Basic information

Entry
Database: PDB / ID: 7t1j
TitleCrystal structure of RUBISCO from Rhodospirillaceae bacterium BRH_c57
ComponentsRibulose bisphosphate carboxylase
KeywordsLYASE / Ribulose-1 / 5-bisphosphate carboxylase-oxygenase
Function / homology
Function and homology information


ribulose-bisphosphate carboxylase / ribulose-bisphosphate carboxylase activity / reductive pentose-phosphate cycle / monooxygenase activity / magnesium ion binding
Similarity search - Function
Ribulose bisphosphate carboxylase large subunit, type II / 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
2-CARBOXYARABINITOL-1,5-DIPHOSPHATE / Ribulose bisphosphate carboxylase
Similarity search - Component
Biological speciesRhodospirillaceae bacterium BRH_c57 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.96 Å
AuthorsPereira, J.H. / Liu, A.K. / Shih, P.M. / Adams, P.D.
Funding support United States, 1items
OrganizationGrant numberCountry
Department of Energy (DOE, United States) United States
CitationJournal: Sci Adv / Year: 2022
Title: Structural plasticity enables evolution and innovation of RuBisCO assemblies.
Authors: Liu, A.K. / Pereira, J.H. / Kehl, A.J. / Rosenberg, D.J. / Orr, D.J. / Chu, S.K.S. / Banda, D.M. / Hammel, M. / Adams, P.D. / Siegel, J.B. / Shih, P.M.
History
DepositionDec 2, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 7, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ribulose bisphosphate carboxylase
B: Ribulose bisphosphate carboxylase
C: Ribulose bisphosphate carboxylase
D: Ribulose bisphosphate carboxylase
E: Ribulose bisphosphate carboxylase
F: Ribulose bisphosphate carboxylase
G: Ribulose bisphosphate carboxylase
H: Ribulose bisphosphate carboxylase
I: Ribulose bisphosphate carboxylase
J: Ribulose bisphosphate carboxylase
K: Ribulose bisphosphate carboxylase
L: Ribulose bisphosphate carboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)610,37236
Polymers605,80712
Non-polymers4,56524
Water80,2214453
1
A: Ribulose bisphosphate carboxylase
B: Ribulose bisphosphate carboxylase
C: Ribulose bisphosphate carboxylase
D: Ribulose bisphosphate carboxylase
G: Ribulose bisphosphate carboxylase
H: Ribulose bisphosphate carboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)305,18618
Polymers302,9046
Non-polymers2,28312
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: Ribulose bisphosphate carboxylase
F: Ribulose bisphosphate carboxylase
I: Ribulose bisphosphate carboxylase
J: Ribulose bisphosphate carboxylase
K: Ribulose bisphosphate carboxylase
L: Ribulose bisphosphate carboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)305,18618
Polymers302,9046
Non-polymers2,28312
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)74.807, 104.978, 369.611
Angle α, β, γ (deg.)90.000, 93.040, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein
Ribulose bisphosphate carboxylase / RuBisCO


Mass: 50483.938 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodospirillaceae bacterium BRH_c57 (bacteria)
Gene: cbbM, VR70_18855 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A0F2R9T6, ribulose-bisphosphate carboxylase
#2: Sugar
ChemComp-CAP / 2-CARBOXYARABINITOL-1,5-DIPHOSPHATE


Type: saccharide / Mass: 356.115 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C6H14O13P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4453 / Source method: isolated from a natural source / Formula: H2O
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: 2.39 Å3/Da / Density % sol: 48.58 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.2 M Magnesium Formate pH 5.9, 20 % PEG 3,350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X17B1 / Wavelength: 0.907936 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 27, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.907936 Å / Relative weight: 1
ReflectionResolution: 1.96→29.52 Å / Num. obs: 399609 / % possible obs: 98.2 % / Redundancy: 1.9 % / Biso Wilson estimate: 27.13 Å2 / CC1/2: 0.982 / Net I/σ(I): 4.81
Reflection shellResolution: 1.96→2.03 Å / Num. unique obs: 35839 / CC1/2: 0.41

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Processing

Software
NameVersionClassification
phenix.refine1.20.1_4487refinement
PHENIX1.20.1_4487refinement
xia2data reduction
xia2data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 9rub

9rub


Resolution: 1.96→29.52 Å / SU ML: 0.2501 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.7648
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2354 2001 0.5 %0.5
Rwork0.1957 397361 --
obs0.1959 399362 98.26 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 35.02 Å2
Refinement stepCycle: LAST / Resolution: 1.96→29.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms42016 0 264 4453 46733
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.004743288
X-RAY DIFFRACTIONf_angle_d0.619658631
X-RAY DIFFRACTIONf_chiral_restr0.04226097
X-RAY DIFFRACTIONf_plane_restr0.00437782
X-RAY DIFFRACTIONf_dihedral_angle_d14.846615619
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.96-2.010.32721230.286624048X-RAY DIFFRACTION83.41
2.01-2.070.31541440.267428661X-RAY DIFFRACTION99.87
2.07-2.130.29381400.253628687X-RAY DIFFRACTION99.87
2.13-2.20.27571550.238428825X-RAY DIFFRACTION99.91
2.2-2.270.26711420.229428724X-RAY DIFFRACTION99.75
2.27-2.370.25441370.220728666X-RAY DIFFRACTION99.86
2.37-2.470.27531480.218528852X-RAY DIFFRACTION99.87
2.47-2.60.26491420.213828745X-RAY DIFFRACTION99.82
2.6-2.770.27631470.214328847X-RAY DIFFRACTION99.63
2.77-2.980.27291450.209128465X-RAY DIFFRACTION98.74
2.98-3.280.23171390.194428518X-RAY DIFFRACTION98.74
3.28-3.750.21191410.172528776X-RAY DIFFRACTION99.24
3.75-4.730.19111480.146428669X-RAY DIFFRACTION98.72
4.73-29.520.18331500.174128878X-RAY DIFFRACTION98.21

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