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- PDB-9i27: activated Form II Rubisco from Rhodospirillum rubrum with bound M... -

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Basic information

Entry
Database: PDB / ID: 9i27
Titleactivated Form II Rubisco from Rhodospirillum rubrum with bound Magnesium and CABP
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
2-CARBOXYARABINITOL-1,5-DIPHOSPHATE / 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,9256
Polymers101,1642
Non-polymers7614
Water7,476415
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10080 Å2
ΔGint-72 kcal/mol
Surface area29150 Å2
Unit cell
Length a, b, c (Å)133.800, 133.800, 151.570
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Ribulose bisphosphate carboxylase / RuBisCO


Mass: 50581.922 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: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#3: Sugar ChemComp-CAP / 2-CARBOXYARABINITOL-1,5-DIPHOSPHATE


Type: saccharide / Mass: 356.115 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O13P2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 415 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 3.87 Å3/Da / Density % sol: 68.23 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.3
Details: Crystallization of activated CbbM in buffer containing 20 mM Tris (pH 8.5), 100 mM NaCl, 0.2 mM CABP, and 10 mM sodium bicarbonate was mixed with a condition containing 200 mM Bis-Tris ...Details: Crystallization of activated CbbM in buffer containing 20 mM Tris (pH 8.5), 100 mM NaCl, 0.2 mM CABP, and 10 mM sodium bicarbonate was mixed with a condition containing 200 mM Bis-Tris propane (pH 7.3) and 20 % (w/v) PEG4000. Prior to plung freezing the crystals in liquid nitrogen the mother liquor was supplemented with 33 % (v/v) PEG200.

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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→29.59 Å / Num. obs: 69625 / % possible obs: 99.4 % / Redundancy: 11.5 % / CC1/2: 0.996 / Rmerge(I) obs: 0.192 / Rrim(I) all: 0.201 / Net I/σ(I): 12.28
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID
2.3-2.361.25551110.8051.3111
2.36-2.420.97649940.8421.021
2.42-2.490.79148870.8840.8271
2.49-2.570.64746870.9180.6771
2.57-2.660.5645840.9330.5881
2.66-2.750.51644400.9490.5391
2.75-2.850.4543130.9640.471
2.85-2.970.37941020.9740.3961
2.97-3.10.3439230.9810.3551
3.1-3.250.26537340.9880.2771
3.25-3.430.20235250.990.2121
3.43-3.640.14733610.9930.1551
3.64-3.890.10732330.9950.1131
3.89-4.20.08230060.9970.0861
4.2-4.60.07327800.9970.0761
4.6-5.140.07325170.9980.0761
5.14-5.940.08222210.9970.0861
5.94-7.270.07618900.9960.081
7.27-10.290.05614890.9980.0591
10.29-29.590.0538280.9980.0561

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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→29.59 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 20.65 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2166 2005 2.88 %
Rwork0.1978 --
obs0.1983 69621 99.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.3→29.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7000 0 44 415 7459
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0037208
X-RAY DIFFRACTIONf_angle_d0.659776
X-RAY DIFFRACTIONf_dihedral_angle_d13.152588
X-RAY DIFFRACTIONf_chiral_restr0.0441034
X-RAY DIFFRACTIONf_plane_restr0.0051294
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.360.27141390.22914780X-RAY DIFFRACTION100
2.36-2.420.23141430.21614824X-RAY DIFFRACTION100
2.42-2.490.24911420.20764807X-RAY DIFFRACTION100
2.49-2.570.22071370.19274790X-RAY DIFFRACTION100
2.57-2.660.22371470.19614823X-RAY DIFFRACTION100
2.66-2.770.21611410.19954820X-RAY DIFFRACTION100
2.77-2.90.24441450.20524816X-RAY DIFFRACTION100
2.9-3.050.24341410.20674811X-RAY DIFFRACTION100
3.05-3.240.23851410.22864763X-RAY DIFFRACTION99
3.24-3.490.23891390.21494719X-RAY DIFFRACTION97
3.49-3.840.22831450.18924829X-RAY DIFFRACTION99
3.84-4.40.18471500.16514892X-RAY DIFFRACTION100
4.4-5.530.16281460.17554909X-RAY DIFFRACTION100
5.53-29.590.21841490.21055033X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: -54.7046 Å / Origin y: 28.855 Å / Origin z: 16.6416 Å
111213212223313233
T0.1579 Å2-0.0288 Å20.0014 Å2-0.1414 Å20.0073 Å2--0.1772 Å2
L0.643 °20.1255 °2-0.2348 °2-0.6497 °20.2019 °2--0.8616 °2
S0.0145 Å °-0.0578 Å °0.0277 Å °0.0506 Å °0.0118 Å °-0.0319 Å °0.0104 Å °0.0779 Å °-0.0082 Å °
Refinement TLS groupSelection details: all

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