9DYR | pdb_00009dyr

Crystal Structure of Rubisco in complex with CABP from Methanococcoides burtonii

PDB DOI: https://doi.org/10.2210/pdb9DYR/pdb

Classification: LIGASE
Organism(s): Methanococcoides burtonii
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2024-10-14 Released: 2025-11-19
Deposition Author(s): Pereira, J.H., Liu, A.K., Shih, P.M., Adams, P.D.
Funding Organization(s): Department of Energy (DOE, United States)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.66 Å
R-Value Free:
0.277 (Depositor), 0.277 (DCC)
R-Value Work:
0.253 (Depositor), 0.253 (DCC)
R-Value Observed:
0.253 (Depositor)

Starting Model: in silico
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Ligand-mediated emergence of higher-order protein complexity

Liu, A.K., Kaeser, B., Pereira, J.H., Taylor-Kearney, L.J., Hammel, M., Nogales, N., Adams, P.D., Shih, P.M.

To be published.

Macromolecule Content

Total Structure Weight: 528.86 kDa
Atom Count: 36,567
Modeled Residue Count: 4,570
Deposited Residue Count: 4,680
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ribulose-1,5-bisphosphate carboxylase	A, B, C, D, E A, B, C, D, E, F, G, H, I, J	468	Methanococcoides burtonii	Mutation(s): 0

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