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- PDB-6ybp: Propionyl-CoA carboxylase of Methylorubrum extorquens with bound CoA -

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Basic information

Entry
Database: PDB / ID: 6ybp
TitlePropionyl-CoA carboxylase of Methylorubrum extorquens with bound CoA
Components
  • Propionyl-CoA carboxylase alpha subunit
  • Propionyl-CoA carboxylase beta chain
KeywordsLIGASE / biotin dependent / ATP dependent / propionyl-CoA / heterododecamer / CO2 fixation
Function / homology
Function and homology information


propionyl-CoA carboxylase / propionyl-CoA carboxylase activity / lipid catabolic process / ATP binding / metal ion binding
Similarity search - Function
Propionyl-coenzyme A carboxylase, BT domain / Propionyl-coenzyme A carboxylase BT domain / : / : / Acetyl-coenzyme A carboxyltransferase, C-terminal / Acetyl-coenzyme A (CoA) carboxyltransferase C-terminal domain profile. / Acetyl-coenzyme A carboxyltransferase, N-terminal / Acetyl-coenzyme A (CoA) carboxyltransferase N-terminal domain profile. / Acetyl-CoA carboxylase / Carboxyl transferase domain ...Propionyl-coenzyme A carboxylase, BT domain / Propionyl-coenzyme A carboxylase BT domain / : / : / Acetyl-coenzyme A carboxyltransferase, C-terminal / Acetyl-coenzyme A (CoA) carboxyltransferase C-terminal domain profile. / Acetyl-coenzyme A carboxyltransferase, N-terminal / Acetyl-coenzyme A (CoA) carboxyltransferase N-terminal domain profile. / Acetyl-CoA carboxylase / Carboxyl transferase domain / Biotin-binding site / Biotin-requiring enzymes attachment site. / Biotin carboxylase-like, N-terminal domain / Biotin carboxylase, C-terminal / Biotin carboxylation domain / Biotin carboxylase, N-terminal domain / Biotin carboxylase C-terminal domain / Biotin carboxylation domain profile. / Biotin carboxylase C-terminal domain / Carbamoyl-phosphate synthase subdomain signature 1. / Carbamoyl-phosphate synthetase large subunit-like, ATP-binding domain / Carbamoyl-phosphate synthase L chain, ATP binding domain / Biotin-requiring enzyme / Rudiment single hybrid motif / Biotinyl/lipoyl domain profile. / Biotin/lipoyl attachment / Single hybrid motif / Pre-ATP-grasp domain superfamily / ATP-grasp fold / ATP-grasp fold profile. / ClpP/crotonase-like domain superfamily / Carbamoyl-phosphate synthase subdomain signature 2.
Similarity search - Domain/homology
Chem-BTI / COENZYME A / Propionyl-CoA carboxylase beta chain / propionyl-CoA carboxylase
Similarity search - Component
Biological speciesMethylorubrum extorquens (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.48 Å
AuthorsSchuller, J.M. / Schuller, S.K. / Zarzycki, J. / Scheffen, M. / Marchal, D.M. / Erb, T.J.
Funding support Germany, 2items
OrganizationGrant numberCountry
European CommissionFET-Open 686330 Germany
German Research Foundation (DFG)SCHU 3364/1-1 Germany
CitationJournal: Nat Catal / Year: 2021
Title: A new-to-nature carboxylation module to improve natural and synthetic CO2 fixation
Authors: Scheffen, M. / Marchal, D.G. / Beneyton, T. / Schuller, S.K. / Klose, M. / Diehl, C. / Lehmann, J. / Pfister, P. / Carrillo, M. / He, H. / Aslan, S. / Cortina, N.S. / Claus, P. / ...Authors: Scheffen, M. / Marchal, D.G. / Beneyton, T. / Schuller, S.K. / Klose, M. / Diehl, C. / Lehmann, J. / Pfister, P. / Carrillo, M. / He, H. / Aslan, S. / Cortina, N.S. / Claus, P. / Bollschweiler, D. / Baret, J.C. / Schuller, J.M. / Zarzycki, J. / Bar-Even, A. / Erb, T.J.
History
DepositionMar 17, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 28, 2020Provider: repository / Type: Initial release
Revision 1.0Oct 28, 2020Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Oct 28, 2020Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Oct 28, 2020Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.0Oct 28, 2020Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Oct 28, 2020Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1May 12, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Apr 9, 2025Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_3d_fitting_list / em_admin / pdbx_entry_details / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type / _em_admin.last_update / _pdbx_entry_details.has_protein_modification
Revision 1.1Apr 9, 2025Data content type: EM metadata
Data content type: EM metadata / EM metadata ...EM metadata / EM metadata / EM metadata / EM metadata
Group: Data processing / Database references ...Data processing / Database references / Experimental summary / Refinement description
Data content type: EM metadata / EM metadata ...EM metadata / EM metadata / EM metadata / EM metadata
Category: database_2 / em_3d_fitting_list ...database_2 / em_3d_fitting_list / em_admin / pdbx_initial_refinement_model
Data content type: EM metadata / EM metadata ...EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type / _em_admin.last_update

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Structure visualization

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Structure viewerMolecule:
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Assembly

Deposited unit
A: Propionyl-CoA carboxylase beta chain
B: Propionyl-CoA carboxylase beta chain
C: Propionyl-CoA carboxylase beta chain
D: Propionyl-CoA carboxylase beta chain
E: Propionyl-CoA carboxylase beta chain
F: Propionyl-CoA carboxylase beta chain
G: Propionyl-CoA carboxylase alpha subunit
H: Propionyl-CoA carboxylase alpha subunit
I: Propionyl-CoA carboxylase alpha subunit
J: Propionyl-CoA carboxylase alpha subunit
K: Propionyl-CoA carboxylase alpha subunit
L: Propionyl-CoA carboxylase alpha subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)774,25724
Polymers768,28212
Non-polymers5,97512
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
Propionyl-CoA carboxylase beta chain


Mass: 56060.008 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methylorubrum extorquens (strain ATCC 14718 / DSM 1338 / JCM 2805 / NCIMB 9133 / AM1) (bacteria)
Gene: pccB, MexAM1_META1p0172 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: C5AP75, propionyl-CoA carboxylase
#2: Protein
Propionyl-CoA carboxylase alpha subunit


Mass: 71986.961 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methylorubrum extorquens (strain ATCC 14718 / DSM 1338 / JCM 2805 / NCIMB 9133 / AM1) (bacteria)
Gene: pccA, MexAM1_META1p3203 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: C5AWU5, propionyl-CoA carboxylase
#3: Chemical
ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#4: Chemical
ChemComp-BTI / 5-(HEXAHYDRO-2-OXO-1H-THIENO[3,4-D]IMIDAZOL-6-YL)PENTANAL


Mass: 228.311 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C10H16N2O2S
Has ligand of interestN
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Propionyl-CoA carboxylase of Methylorubrum extorquens with bound CoA
Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT
Molecular weightValue: 0.74 MDa / Experimental value: YES
Source (natural)Organism: Methylorubrum extorquens (strain ATCC 14718 / DSM 1338 / JCM 2805 / NCIMB 9133 / AM1) (bacteria)
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria)
Buffer solutionpH: 7.8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE-PROPANE

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Electron microscopy imaging

MicroscopyModel: TFS GLACIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 50.2 e/Å2 / Film or detector model: GATAN K2 BASE (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.17.1_3660: / Classification: refinement
EM software
IDNameVersionCategory
7UCSF Chimera1.13.1model fitting
9PHENIX1.17.1-3660-00model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.48 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 77714 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL
Atomic model buildingPDB-ID: 3N6R

3n6r


Accession code: 3N6R / Source name: PDB / Type: experimental model
RefinementStereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 99.83 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.008437078
ELECTRON MICROSCOPYf_angle_d0.761250178
ELECTRON MICROSCOPYf_chiral_restr0.05215635
ELECTRON MICROSCOPYf_plane_restr0.00776569
ELECTRON MICROSCOPYf_dihedral_angle_d24.290413725

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