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- PDB-7t1c: Crystal structure of RUBISCO from Sulfurivirga caldicuralii -

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Basic information

Entry
Database: PDB / ID: 7t1c
TitleCrystal structure of RUBISCO from Sulfurivirga caldicuralii
ComponentsRibulose-bisphosphate carboxylase
KeywordsLYASE / Ribulose-1 / 5-bisphosphate carboxylase-oxygenase
Function / homology
Function and homology information


ribulose-bisphosphate carboxylase / ribulose-bisphosphate carboxylase activity / carbon fixation / magnesium ion binding
Similarity search - Function
Ribulose bisphosphate carboxylase large subunit, type II / 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
Ribulose bisphosphate carboxylase
Similarity search - Component
Biological speciesSulfurivirga caldicuralii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.73 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 1, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ribulose-bisphosphate carboxylase


Theoretical massNumber of molelcules
Total (without water)51,7221
Polymers51,7221
Non-polymers00
Water5,405300
1
A: Ribulose-bisphosphate carboxylase

A: Ribulose-bisphosphate carboxylase

A: Ribulose-bisphosphate carboxylase

A: Ribulose-bisphosphate carboxylase


Theoretical massNumber of molelcules
Total (without water)206,8904
Polymers206,8904
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_665-x+1,-y+1,z1
crystal symmetry operation7_556y,x,-z+5/31
crystal symmetry operation10_666-y+1,-x+1,-z+5/31
Unit cell
Length a, b, c (Å)133.056, 133.056, 112.456
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number180
Space group name H-MP6222
Space group name HallP622(x,y,z+1/3)
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/3
#3: y,-x+y,z+2/3
#4: -y,x-y,z+2/3
#5: -x+y,-x,z+1/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+1/3
#8: -x,-y,z
#9: y,x,-z+2/3
#10: -y,-x,-z+2/3
#11: -x+y,y,-z
#12: x,x-y,-z+1/3
Components on special symmetry positions
IDModelComponents
11A-505-

HOH

21A-658-

HOH

31A-741-

HOH

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Components

#1: Protein Ribulose-bisphosphate carboxylase


Mass: 51722.469 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfurivirga caldicuralii (bacteria) / Gene: SAMN05443662_0203 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A1N6DK16, ribulose-bisphosphate carboxylase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 300 / 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: 2.78 Å3/Da / Density % sol: 55.72 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.05 M Citric acid, 0.05 M Bis-TRIS propane pH 5.0, 16 % PEG 3,350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 15, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.73→43.55 Å / Num. obs: 61467 / % possible obs: 100 % / Redundancy: 19.4 % / Biso Wilson estimate: 27.6 Å2 / CC1/2: 0.999 / Net I/σ(I): 15.9
Reflection shellResolution: 1.73→1.79 Å / Num. unique obs: 6044 / CC1/2: 0.35

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6IUS

6ius


Resolution: 1.73→43.55 Å / SU ML: 0.1858 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 21.029
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1844 1776 3.23 %
Rwork0.1661 53214 -
obs0.1667 54990 89.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 40.92 Å2
Refinement stepCycle: LAST / Resolution: 1.73→43.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3538 0 0 300 3838
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00373636
X-RAY DIFFRACTIONf_angle_d0.72844912
X-RAY DIFFRACTIONf_chiral_restr0.0423496
X-RAY DIFFRACTIONf_plane_restr0.0079649
X-RAY DIFFRACTIONf_dihedral_angle_d5.6981489
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.73-1.780.3833910.37153155X-RAY DIFFRACTION69.75
1.78-1.830.30471190.32243319X-RAY DIFFRACTION74
1.83-1.890.29871240.27493538X-RAY DIFFRACTION78.91
1.89-1.960.23461290.22573743X-RAY DIFFRACTION82.35
1.96-2.030.25961310.19663902X-RAY DIFFRACTION87.22
2.03-2.130.20221300.18094119X-RAY DIFFRACTION90.99
2.13-2.240.20731400.17014197X-RAY DIFFRACTION92.24
2.24-2.380.18121410.15954281X-RAY DIFFRACTION94.11
2.38-2.560.16561470.1554401X-RAY DIFFRACTION96.01
2.56-2.820.18871490.15534468X-RAY DIFFRACTION97.9
2.82-3.230.19771530.16084548X-RAY DIFFRACTION98.45
3.23-4.070.15941570.14354640X-RAY DIFFRACTION99.56
4.07-43.550.15751650.15414903X-RAY DIFFRACTION99.78
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
15.667272679731.81475024024-1.405530152793.211457402110.05269454688333.31172427853-0.01213254963760.5635528412370.0153853253868-0.1446945603090.001858617877410.2732887121870.149159775457-0.459422147730.0006833952576950.215537927087-0.0011482046272-0.03667561203880.322185051191-0.08121237319150.25142494097418.031708427329.035519832870.9408783263
20.5221756443940.02319843387990.0710321825040.806057996630.3509660783861.00434605627-0.0160459767225-0.0269994071799-0.08554787231960.1578135574320.00933922866888-0.05071108312350.1838801516830.0462679603827-0.001420367854850.2104766875580.05491468033080.006279637167590.217193480126-0.0005900720464120.257919343135.035664335837.597205197497.1934710709
31.20798569729-0.8474517083371.454780983461.50660720963-0.2905829448152.828996705540.0700152984548-0.236390627272-0.2880385686910.4385022463360.0341560211986-0.06728705698140.849722725594-0.111610437213-0.1376590002530.5795772409580.0765140572444-0.01556773010480.2797384840970.03456751347260.34469868108843.608630325720.5708849058101.36445426
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 2 through 69 )2 - 691 - 59
22chain 'A' and (resid 70 through 311 )70 - 31160 - 301
33chain 'A' and (resid 312 through 463 )312 - 463302 - 453

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