8QMW

Non-obligately L8S8-complex forming RubisCO derived from ancestral sequence reconstruction and rational engineering in L8S8 complex with substitutions R269W, E271R, L273N

PDB DOI: https://doi.org/10.2210/pdb8QMW/pdb

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

Deposited: 2023-09-25 Released: 2024-10-02
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: 1.75 Å
R-Value Free: 0.174
R-Value Work: 0.145
R-Value Observed: 0.145

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 protein-protein interactions

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

(2024) EMBO J

Macromolecule Content

Total Structure Weight: 256.35 kDa
Atom Count: 19,717
Modelled Residue Count: 2,206
Deposited Residue Count: 2,248
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(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

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
RubisCO small subunit	E, F, G, H	105	synthetic construct	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 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 I [auth A] SDF format, chain M [auth C] SDF format, chain P [auth D] SDF format, chain K [auth B] MOL2 format, chain I [auth A] MOL2 format, chain M [auth C] MOL2 format, chain P [auth D] MOL2 format, chain K [auth B] mmCIF format, chain I [auth A] mmCIF format, chain M [auth C] mmCIF format, chain P [auth D] mmCIF format, chain K [auth B]	I [auth A], K [auth B], M [auth C], P [auth D]	2-CARBOXYARABINITOL-1,5-DIPHOSPHATE C₆ H₁₄ O₁₃ P₂ ITHCSGCUQDMYAI-ZMIZWQJLSA-N		Interactions Focus chain I [auth A] Focus chain K [auth B] Focus chain M [auth C] Focus chain P [auth D] Interactions & Density Focus chain I [auth A] Focus chain K [auth B] Focus chain M [auth C] Focus chain P [auth D]
B3P Query on B3P Download Ideal Coordinates CCD File SDF format, chain O [auth C] MOL2 format, chain O [auth C] mmCIF format, chain O [auth C]	O [auth C]	2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C₁₁ H₂₆ N₂ O₆ HHKZCCWKTZRCCL-UHFFFAOYSA-N		Interactions Focus chain O [auth C] Interactions & Density Focus chain O [auth C]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain Q [auth D] SDF format, chain J [auth A] SDF format, chain L [auth B] SDF format, chain N [auth C] MOL2 format, chain Q [auth D] MOL2 format, chain J [auth A] MOL2 format, chain L [auth B] MOL2 format, chain N [auth C] mmCIF format, chain Q [auth D] mmCIF format, chain J [auth A] mmCIF format, chain L [auth B] mmCIF format, chain N [auth C]	J [auth A], L [auth B], N [auth C], Q [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Focus chain L [auth B] Focus chain N [auth C] Focus chain Q [auth D] Interactions & Density Focus chain J [auth A] Focus chain L [auth B] Focus chain N [auth C] Focus chain Q [auth D]