6YBP

Propionyl-CoA carboxylase of Methylorubrum extorquens with bound CoA

PDB DOI: https://doi.org/10.2210/pdb6YBP/pdb
EM Map EMD-10770: EMDB EMDataResource

Classification: LIGASE
Organism(s): Methylorubrum extorquens AM1
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2020-03-17 Released: 2020-10-28
Deposition Author(s): Schuller, J.M., Schuller, S.K., Zarzycki, J., Scheffen, M., Marchal, D.M., Erb, T.J.
Funding Organization(s): European Commission, German Research Foundation (DFG)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.48 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

A new-to-nature carboxylation module to improve natural and synthetic CO2 fixation

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.

(2021) Nat Catal

DOI: https://doi.org/10.1038/s41929-020-00557-y

Macromolecule Content

Total Structure Weight: 774.26 kDa
Atom Count: 36,410
Modelled Residue Count: 4,702
Deposited Residue Count: 7,062
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Propionyl-CoA carboxylase beta chain	A, B, C, D, E A, B, C, D, E, F	510	Methylorubrum extorquens AM1	Mutation(s): 0 Gene Names: pccB, MexAM1_META1p0172 EC: 6.4.1.3
UniProt
Find proteins for C5AP75 (Methylorubrum extorquens (strain ATCC 14718 / DSM 1338 / JCM 2805 / NCIMB 9133 / AM1)) Explore C5AP75 Go to UniProtKB: C5AP75
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	C5AP75
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Propionyl-CoA carboxylase alpha subunit	G, H, I, J, K G, H, I, J, K, L	667	Methylorubrum extorquens AM1	Mutation(s): 0 Gene Names: pccA, MexAM1_META1p3203 EC: 6.4.1.3
UniProt
Find proteins for C5AWU5 (Methylorubrum extorquens (strain ATCC 14718 / DSM 1338 / JCM 2805 / NCIMB 9133 / AM1)) Explore C5AWU5 Go to UniProtKB: C5AWU5
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	C5AWU5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
COA Query on COA Download Ideal Coordinates CCD File SDF format, chain M [auth A] SDF format, chain N [auth B] SDF format, chain O [auth C] SDF format, chain P [auth D] SDF format, chain Q [auth E] SDF format, chain R [auth F] MOL2 format, chain M [auth A] MOL2 format, chain N [auth B] MOL2 format, chain O [auth C] MOL2 format, chain P [auth D] MOL2 format, chain Q [auth E] MOL2 format, chain R [auth F]	M [auth A] N [auth B] O [auth C] P [auth D] Q [auth E] M [auth A], N [auth B], O [auth C], P [auth D], Q [auth E], R [auth F]	COENZYME A C₂₁ H₃₆ N₇ O₁₆ P₃ S RGJOEKWQDUBAIZ-IBOSZNHHSA-N		Interactions Focus chain M [auth A] Focus chain N [auth B] Focus chain O [auth C] Focus chain P [auth D] Focus chain Q [auth E] Focus chain R [auth F] Interactions & Density Focus chain M [auth A] Focus chain N [auth B] Focus chain O [auth C] Focus chain P [auth D] Focus chain Q [auth E] Focus chain R [auth F]
BTI Query on BTI Download Ideal Coordinates CCD File SDF format, chain S [auth G] SDF format, chain T [auth H] SDF format, chain U [auth I] SDF format, chain V [auth J] SDF format, chain W [auth K] SDF format, chain X [auth L] MOL2 format, chain S [auth G] MOL2 format, chain T [auth H] MOL2 format, chain U [auth I] MOL2 format, chain V [auth J] MOL2 format, chain W [auth K] MOL2 format, chain X [auth L]	S [auth G] T [auth H] U [auth I] V [auth J] W [auth K] S [auth G], T [auth H], U [auth I], V [auth J], W [auth K], X [auth L]	5-(HEXAHYDRO-2-OXO-1H-THIENO[3,4-D]IMIDAZOL-6-YL)PENTANAL C₁₀ H₁₆ N₂ O₂ S ARDNWGMSCXSPBF-CIUDSAMLSA-N		Interactions Focus chain S [auth G] Focus chain T [auth H] Focus chain U [auth I] Focus chain V [auth J] Focus chain W [auth K] Focus chain X [auth L] Interactions & Density Focus chain S [auth G] Focus chain T [auth H] Focus chain U [auth I] Focus chain V [auth J] Focus chain W [auth K] Focus chain X [auth L]