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- PDB-8qmv: L2 forming RubisCO derived from ancestral sequence reconstruction... -

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Basic information

Entry
Database: PDB / ID: 8qmv
TitleL2 forming RubisCO derived from ancestral sequence reconstruction of the last common ancestor of Form I'' and Form I RubisCOs
ComponentsRubisCO large subunit
KeywordsLYASE / RubisCO / CABP / ancestral
Function / homology2-CARBOXYARABINITOL-1,5-DIPHOSPHATE
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsZarzycki, J. / Schulz, L. / Erb, T.J. / Hochberg, G.K.A.
Funding support Germany, 2items
OrganizationGrant numberCountry
Max Planck Society Germany
Joachim Herz Stiftung Germany
Citation
Journal: Embo J. / Year: 2025
Title: Layered entrenchment maintains essentiality in the evolution of Form I Rubisco complexes.
Authors: Schulz, L. / Zarzycki, J. / Steinchen, W. / Hochberg, G.K.A. / Erb, T.J.
#1: Journal: Biorxiv / Year: 2024
Title: Layered entrenchment maintains essentiality in the evolution of Form I Rubisco complexes
Authors: Schulz, L. / Zarzycki, J. / Steinchen, W. / Hochberg, G.K.A. / Erb, T.J.
History
DepositionSep 25, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 16, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 27, 2024Group: Database references / Category: citation / citation_author
Revision 1.2Jan 15, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RubisCO large subunit
B: RubisCO large subunit
C: RubisCO large subunit
D: RubisCO large subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)206,14512
Polymers204,6234
Non-polymers1,5228
Water20,7711153
1
A: RubisCO large subunit
B: RubisCO large subunit
hetero molecules


  • defined by author&software
  • Evidence: light scattering, Froms a L2 dimer in the absence of bound CABP in solution with 109 kDa in mass photometry experiments. In the presence of CABP an L8 octamer forms in solution with 442 kDa ...Evidence: light scattering, Froms a L2 dimer in the absence of bound CABP in solution with 109 kDa in mass photometry experiments. In the presence of CABP an L8 octamer forms in solution with 442 kDa in mass photometry experiments., gel filtration, Froms a L2 dimer in the absence of bound CABP in solution. In the presence of CABP an L8 octamer is formed in solution.
  • 103 kDa, 2 polymers
  • Search similar-shape structures of this assembly by Omokage search (details)
Theoretical massNumber of molelcules
Total (without water)103,0736
Polymers102,3122
Non-polymers7614
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10470 Å2
ΔGint-73 kcal/mol
Surface area27200 Å2
MethodPISA
2
C: RubisCO large subunit
D: RubisCO large subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,0736
Polymers102,3122
Non-polymers7614
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10550 Å2
ΔGint-73 kcal/mol
Surface area27300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.790, 203.800, 147.370
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-773-

HOH

21A-785-

HOH

31A-881-

HOH

41A-896-

HOH

51D-879-

HOH

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Components

#1: Protein
RubisCO large subunit


Mass: 51155.840 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: ribulose-bisphosphate carboxylase
#2: Sugar
ChemComp-CAP / 2-CARBOXYARABINITOL-1,5-DIPHOSPHATE


Type: saccharide / Mass: 356.115 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: C6H14O13P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1153 / 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: 2.24 Å3/Da / Density % sol: 45 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: Purified enzyme (10 mg/mL) in 25 mM Tricine-NaOH, 75 mM NaCl, pH 8.0 was incubated at 3% (v/v) CO2 in air and 30 degrees C for 1 hour in the presence of 0.3 mM CABP and 4.8 mM MgCl2. The ...Details: Purified enzyme (10 mg/mL) in 25 mM Tricine-NaOH, 75 mM NaCl, pH 8.0 was incubated at 3% (v/v) CO2 in air and 30 degrees C for 1 hour in the presence of 0.3 mM CABP and 4.8 mM MgCl2. The enzyme was then mixed in a 1:1 ratio with 0.1 M TRIS pH 8.5, 0.2 M magnesium chloride, 30 % (v/v) polyethylene glycol 400. The crystals were flash 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: P14 (MX2) / Wavelength: 0.6888 Å
DetectorType: DECTRIS EIGER2 X CdTe 16M / Detector: PIXEL / Date: Dec 2, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.6888 Å / Relative weight: 1
ReflectionResolution: 1.85→24.97 Å / Num. obs: 155284 / % possible obs: 99.9 % / Redundancy: 13.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.113 / Rrim(I) all: 0.117 / Net I/σ(I): 16.04
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID
1.85-1.91.077113290.731.1261
1.9-1.950.919111500.8510.9531
1.95-2.010.756107810.8880.7841
2.01-2.070.586104860.9360.6081
2.07-2.140.5102370.9520.5181
2.14-2.210.41898710.9640.4341
2.21-2.290.3595230.9750.3631
2.29-2.390.28191940.9850.2911
2.39-2.490.24187990.9880.251
2.49-2.620.20284270.9920.2091
2.62-2.760.16280310.9940.1681
2.76-2.930.13375690.9960.1381
2.93-3.130.10971920.9970.1131
3.13-3.380.0866800.9980.0831
3.38-3.70.06361520.9990.0651
3.7-4.140.04955550.9990.0511
4.14-4.780.041497310.0431
4.78-5.850.04442060.9990.0451
5.85-8.270.041330010.0431
8.27-24.970.034182910.0361

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
XSCALEdata scaling
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.85→24.97 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 17.98 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1739 1999 1.29 %
Rwork0.1607 --
obs0.1609 155237 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.85→24.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14174 0 88 1153 15415
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00314613
X-RAY DIFFRACTIONf_angle_d0.66619817
X-RAY DIFFRACTIONf_dihedral_angle_d12.2455335
X-RAY DIFFRACTIONf_chiral_restr0.0452082
X-RAY DIFFRACTIONf_plane_restr0.0082605
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.90.291360.25210779X-RAY DIFFRACTION99
1.9-1.950.24641400.219210891X-RAY DIFFRACTION100
1.95-20.21091400.205110818X-RAY DIFFRACTION100
2-2.070.22521480.182910879X-RAY DIFFRACTION100
2.07-2.140.20651360.17810901X-RAY DIFFRACTION100
2.14-2.230.19911370.172210903X-RAY DIFFRACTION100
2.23-2.330.19241510.166510905X-RAY DIFFRACTION100
2.33-2.450.18191410.165410910X-RAY DIFFRACTION100
2.45-2.610.17571400.167210902X-RAY DIFFRACTION100
2.61-2.810.19141470.166910944X-RAY DIFFRACTION100
2.81-3.090.16311430.170310972X-RAY DIFFRACTION100
3.09-3.540.17291420.162511014X-RAY DIFFRACTION100
3.54-4.450.14211450.132511076X-RAY DIFFRACTION100
4.45-24.970.14881530.140911344X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 17.8701 Å / Origin y: 58.0125 Å / Origin z: -19.673 Å
111213212223313233
T0.1857 Å2-0.0024 Å2-0.0097 Å2-0.221 Å2-0.0007 Å2--0.1971 Å2
L0.1562 °20.0017 °20.0058 °2-0.2296 °2-0.0232 °2--0.2374 °2
S0.0023 Å °-0.0072 Å °-0.0274 Å °0.0188 Å °-0.0047 Å °-0.0164 Å °0.0401 Å °0.0454 Å °0.0023 Å °
Refinement TLS groupSelection details: all

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