8QMV

L2 forming RubisCO derived from ancestral sequence reconstruction of the last common ancestor of Form I'' and Form I RubisCOs

PDB DOI: https://doi.org/10.2210/pdb8QMV/pdb

Classification: LYASE
Organism(s): synthetic construct
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2023-09-25 Released: 2024-10-16
Deposition Author(s): Zarzycki, J., Schulz, L., Erb, T.J., Hochberg, G.K.A.
Funding Organization(s): Max Planck Society, Joachim Herz Stiftung

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.85 Å
R-Value Free: 0.174
R-Value Work: 0.161
R-Value Observed: 0.161

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Layered entrenchment maintains essentiality in the evolution of Form I Rubisco complexes

Schulz, L., Zarzycki, J., Steinchen, W., Hochberg, G.K.A., Erb, T.J.

(2024) bioRxiv

DOI: https://doi.org/10.1101/2024.01.18.576253

Macromolecule Content

Total Structure Weight: 206.15 kDa
Atom Count: 15,421
Modelled Residue Count: 1,796
Deposited Residue Count: 1,828
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RubisCO large subunit	A, B, C, D	457	synthetic construct	Mutation(s): 0 EC: 4.1.1.39
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
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 E [auth A] SDF format, chain G [auth B] SDF format, chain I [auth C] SDF format, chain K [auth D] MOL2 format, chain E [auth A] MOL2 format, chain G [auth B] MOL2 format, chain I [auth C] MOL2 format, chain K [auth D] mmCIF format, chain E [auth A] mmCIF format, chain G [auth B] mmCIF format, chain I [auth C] mmCIF format, chain K [auth D]	E [auth A], G [auth B], I [auth C], K [auth D]	2-CARBOXYARABINITOL-1,5-DIPHOSPHATE C₆ H₁₄ O₁₃ P₂ ITHCSGCUQDMYAI-ZMIZWQJLSA-N		Interactions Focus chain E [auth A] Focus chain G [auth B] Focus chain I [auth C] Focus chain K [auth D] Interactions & Density Focus chain E [auth A] Focus chain G [auth B] Focus chain I [auth C] Focus chain K [auth D]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain H [auth B] SDF format, chain J [auth C] SDF format, chain L [auth D] MOL2 format, chain F [auth A] MOL2 format, chain H [auth B] MOL2 format, chain J [auth C] MOL2 format, chain L [auth D] mmCIF format, chain F [auth A] mmCIF format, chain H [auth B] mmCIF format, chain J [auth C] mmCIF format, chain L [auth D]	F [auth A], H [auth B], J [auth C], L [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain L [auth D] Interactions & Density Focus chain F [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain L [auth D]