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- PDB-9i26: inactive Form II Rubisco from Rhodospirillum rubrum -

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Basic information

Entry
Database: PDB / ID: 9i26
Titleinactive Form II Rubisco from Rhodospirillum rubrum
ComponentsRibulose bisphosphate carboxylase
KeywordsLYASE / ribulose-1 / 5-bisphosphate carboxylase/oxygenase / Rubisco
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
Ribulose bisphosphate carboxylase
Similarity search - Component
Biological speciesRhodospirillum rubrum ATCC 11170 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsKueffner, A.M. / Zarzycki, J. / Erb, T.J.
Funding supportEuropean Union, Germany, 3items
OrganizationGrant numberCountry
European Molecular Biology Organization (EMBO)ALTF 684-2022European Union
Marie Sklodowska-Curie Actions, FragNET ITN101106795 - ECOFixEuropean Union
Max Planck Society Germany
CitationJournal: To Be Published
Title: Bottom-up reconstruction of minimal pyrenoids provides insights into the evolution and mechanisms of carbon concentration by EPYC1 proteins
Authors: Kueffner, A.M. / Pommerkenke, B. / Kley, L. / Ng, J.Z.Y. / Prinz, S. / Tinzl-Zechner, M. / Claus, P. / Paczia, N. / Zarzycki, J. / Hochberg, G.K.A. / Erb, T.J.
History
DepositionJan 20, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 4, 2026Provider: repository / Type: Initial release

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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


Theoretical massNumber of molelcules
Total (without water)101,0782
Polymers101,0782
Non-polymers00
Water2,792155
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4320 Å2
ΔGint-21 kcal/mol
Surface area30240 Å2
Unit cell
Length a, b, c (Å)78.980, 78.980, 277.230
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Ribulose bisphosphate carboxylase / RuBisCO


Mass: 50538.918 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodospirillum rubrum ATCC 11170 (bacteria)
Gene: cbbM, Rru_A2400 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q2RRP5, ribulose-bisphosphate carboxylase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 155 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 2.14 Å3/Da / Density % sol: 42.49 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6
Details: Inactive CbbM in 20 mM Tris buffer (pH 8.5), containing 100 mM NaCl was mixed with condition comprised of 1.2 M ammonium chloride, 100 mM MES (pH 6), 20 %(w/v) PEG6000 in a 1:1 ratio with a ...Details: Inactive CbbM in 20 mM Tris buffer (pH 8.5), containing 100 mM NaCl was mixed with condition comprised of 1.2 M ammonium chloride, 100 mM MES (pH 6), 20 %(w/v) PEG6000 in a 1:1 ratio with a final drop volume of 1 micro liter. The mother liquor was supplemented with 30% (v/v) PEG200, before the crystals were plunge frozen in liquid nitrogen

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.9762 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 10, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 2.3→29.45 Å / Num. obs: 40094 / % possible obs: 99.8 % / Redundancy: 26.38 % / CC1/2: 1 / Rmerge(I) obs: 0.131 / Rrim(I) all: 0.134 / Net I/σ(I): 24.95
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID
2.3-2.361.36428980.6561.3891
2.36-2.421.03128420.7931.051
2.42-2.490.84227470.8540.8571
2.49-2.570.68626930.9050.6991
2.57-2.660.58526080.9380.5961
2.66-2.750.49725150.9630.5061
2.75-2.850.39524610.9750.4031
2.85-2.970.33723420.9850.3431
2.97-3.10.30722760.9920.3121
3.1-3.250.27421350.9960.2791
3.25-3.430.18820720.9970.1911
3.43-3.640.13119440.9980.1331
3.64-3.890.09318600.9990.0941
3.89-4.20.06617460.9990.0681
4.2-4.60.05316050.9990.0541
4.6-5.140.047147610.0481
5.14-5.940.05113090.9990.0521
5.94-7.270.046113710.0471
7.27-10.290.03290210.0331
10.29-29.450.03152610.0311

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Processing

Software
NameVersionClassification
PHENIX(1.21.2_5419: ???)refinement
XSCALEdata scaling
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→29.45 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 20.84 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2263 2000 4.99 %
Rwork0.2036 --
obs0.2048 40091 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.3→29.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6369 0 0 155 6524
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0026523
X-RAY DIFFRACTIONf_angle_d0.4428829
X-RAY DIFFRACTIONf_dihedral_angle_d10.4972325
X-RAY DIFFRACTIONf_chiral_restr0.039932
X-RAY DIFFRACTIONf_plane_restr0.0041162
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.360.31131390.26762647X-RAY DIFFRACTION100
2.36-2.420.29311410.25692682X-RAY DIFFRACTION100
2.42-2.490.2661400.25112668X-RAY DIFFRACTION100
2.49-2.570.24851400.23582670X-RAY DIFFRACTION100
2.57-2.660.28041400.22482678X-RAY DIFFRACTION100
2.66-2.770.27121410.22332674X-RAY DIFFRACTION100
2.77-2.90.23221410.21682694X-RAY DIFFRACTION100
2.9-3.050.25841430.22352708X-RAY DIFFRACTION100
3.05-3.240.30231410.24862673X-RAY DIFFRACTION100
3.24-3.490.24391410.22882712X-RAY DIFFRACTION99
3.49-3.840.23141440.20152736X-RAY DIFFRACTION100
3.84-4.40.18691460.17092774X-RAY DIFFRACTION100
4.4-5.530.17091470.16112794X-RAY DIFFRACTION100
5.53-29.450.20141560.18862981X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 47.6283 Å / Origin y: 36.4663 Å / Origin z: 111.2574 Å
111213212223313233
T0.2534 Å20.0018 Å20.0192 Å2-0.1981 Å2-0.0396 Å2--0.2652 Å2
L0.7142 °2-0.054 °2-0.2298 °2-0.6137 °20.0451 °2--1.0153 °2
S-0.0105 Å °0.054 Å °-0.1282 Å °-0.0506 Å °-0.0065 Å °0.0745 Å °0.0072 Å °-0.0142 Å °-0.0063 Å °
Refinement TLS groupSelection details: all

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