8VGS | pdb_00008vgs

CABP-bound Decameric Rubisco from Candidatus Methanofastidiosum methylthiophilus

PDB DOI: https://doi.org/10.2210/pdb8VGS/pdb
EM Map EMD-43223: EMDB EMDataResource

Classification: LYASE
Organism(s): Candidatus Methanofastidiosum methylothiophilum
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2023-12-27 Released: 2025-03-19
Deposition Author(s): Kaeser, B.P., Liu, A.K., Shih, P.M.
Funding Organization(s): Howard Hughes Medical Institute (HHMI), Department of Energy (DOE, United States)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.14 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

CABP-bound Decameric Rubisco from Candidatus Methanofastidiosum methylthiophilus

Kaeser, B.P., Liu, A.K.

To be published.

Macromolecule Content

Total Structure Weight: 532.71 kDa
Atom Count: 37,097
Modeled Residue Count: 4,680
Deposited Residue Count: 4,750
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribulose bisphosphate carboxylase	A, B, C, D, E A, B, C, D, E, F, G, H, I, J	475	Candidatus Methanofastidiosum methylothiophilum	Mutation(s): 0 Gene Names: rbcL, APG10_01785, APG11_00293 EC: 4.1.1.39
UniProt
Find proteins for A0A150IHQ4 (Candidatus Methanofastidiosum methylothiophilum) Explore A0A150IHQ4 Go to UniProtKB: A0A150IHQ4
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A150IHQ4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CAP (Subject of Investigation/LOI) Query on CAP Download Ideal Coordinates CCD File SDF format, chain CA [auth F] SDF format, chain EA [auth G] SDF format, chain GA [auth H] SDF format, chain N [auth A] SDF format, chain NA [auth J] SDF format, chain R [auth B] SDF format, chain U [auth C] SDF format, chain Z [auth E] SDF format, chain X [auth D] SDF format, chain KA [auth I] MOL2 format, chain CA [auth F] MOL2 format, chain EA [auth G] MOL2 format, chain GA [auth H] MOL2 format, chain N [auth A] MOL2 format, chain NA [auth J] MOL2 format, chain R [auth B] MOL2 format, chain U [auth C] MOL2 format, chain Z [auth E] MOL2 format, chain X [auth D] MOL2 format, chain KA [auth I] mmCIF format, chain CA [auth F] mmCIF format, chain EA [auth G] mmCIF format, chain GA [auth H] mmCIF format, chain N [auth A] mmCIF format, chain NA [auth J] mmCIF format, chain R [auth B] mmCIF format, chain U [auth C] mmCIF format, chain Z [auth E] mmCIF format, chain X [auth D] mmCIF format, chain KA [auth I]	CA [auth F] EA [auth G] GA [auth H] KA [auth I] N [auth A] CA [auth F], EA [auth G], GA [auth H], KA [auth I], N [auth A], NA [auth J], R [auth B], U [auth C], X [auth D], Z [auth E]	2-CARBOXYARABINITOL-1,5-DIPHOSPHATE C₆ H₁₄ O₁₃ P₂ ITHCSGCUQDMYAI-ZMIZWQJLSA-N		Interactions Focus chain CA [auth F] Focus chain EA [auth G] Focus chain GA [auth H] Focus chain KA [auth I] Focus chain N [auth A] Focus chain NA [auth J] Focus chain R [auth B] Focus chain U [auth C] Focus chain X [auth D] Focus chain Z [auth E] Interactions & Density Focus chain CA [auth F] Focus chain EA [auth G] Focus chain GA [auth H] Focus chain KA [auth I] Focus chain N [auth A] Focus chain NA [auth J] Focus chain R [auth B] Focus chain U [auth C] Focus chain X [auth D] Focus chain Z [auth E]
MG (Subject of Investigation/LOI) Query on MG Download Ideal Coordinates CCD File SDF format, chain BA [auth F] SDF format, chain DA [auth G] SDF format, chain FA [auth H] SDF format, chain HA [auth I] SDF format, chain IA [auth I] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain MA [auth J] SDF format, chain O [auth B] SDF format, chain P [auth B] SDF format, chain Q [auth B] SDF format, chain S [auth C] SDF format, chain T [auth C] SDF format, chain V [auth D] SDF format, chain W [auth D] SDF format, chain Y [auth E] SDF format, chain LA [auth J] SDF format, chain K [auth A] SDF format, chain JA [auth I] SDF format, chain AA [auth F] MOL2 format, chain BA [auth F] MOL2 format, chain DA [auth G] MOL2 format, chain FA [auth H] MOL2 format, chain HA [auth I] MOL2 format, chain IA [auth I] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain MA [auth J] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain S [auth C] MOL2 format, chain T [auth C] MOL2 format, chain V [auth D] MOL2 format, chain W [auth D] MOL2 format, chain Y [auth E] MOL2 format, chain LA [auth J] MOL2 format, chain K [auth A] MOL2 format, chain JA [auth I] MOL2 format, chain AA [auth F] mmCIF format, chain BA [auth F] mmCIF format, chain DA [auth G] mmCIF format, chain FA [auth H] mmCIF format, chain HA [auth I] mmCIF format, chain IA [auth I] mmCIF format, chain L [auth A] mmCIF format, chain M [auth A] mmCIF format, chain MA [auth J] mmCIF format, chain O [auth B] mmCIF format, chain P [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain S [auth C] mmCIF format, chain T [auth C] mmCIF format, chain V [auth D] mmCIF format, chain W [auth D] mmCIF format, chain Y [auth E] mmCIF format, chain LA [auth J] mmCIF format, chain K [auth A] mmCIF format, chain JA [auth I] mmCIF format, chain AA [auth F]	AA [auth F] BA [auth F] DA [auth G] FA [auth H] HA [auth I] AA [auth F], BA [auth F], DA [auth G], FA [auth H], HA [auth I], IA [auth I], JA [auth I], K [auth A], L [auth A], LA [auth J], M [auth A], MA [auth J], O [auth B], P [auth B], Q [auth B], S [auth C], T [auth C], V [auth D], W [auth D], Y [auth E]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain AA [auth F] Focus chain BA [auth F] Focus chain DA [auth G] Focus chain FA [auth H] Focus chain HA [auth I] Focus chain IA [auth I] Focus chain JA [auth I] Focus chain K [auth A] Focus chain L [auth A] Focus chain LA [auth J] Focus chain M [auth A] Focus chain MA [auth J] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain S [auth C] Focus chain T [auth C] Focus chain V [auth D] Focus chain W [auth D] Focus chain Y [auth E] Interactions & Density Focus chain AA [auth F] Focus chain BA [auth F] Focus chain DA [auth G] Focus chain FA [auth H] Focus chain HA [auth I] Focus chain IA [auth I] Focus chain JA [auth I] Focus chain K [auth A] Focus chain L [auth A] Focus chain LA [auth J] Focus chain M [auth A] Focus chain MA [auth J] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain S [auth C] Focus chain T [auth C] Focus chain V [auth D] Focus chain W [auth D] Focus chain Y [auth E]