8JON

Structure of a synthetic circadian clock protein KaiC mutant of cyanobacteria Synechococcus elongatus PCC 7942

PDB DOI: https://doi.org/10.2210/pdb8JON/pdb
EM Map EMD-36461: EMDB EMDataResource

Classification: BIOSYNTHETIC PROTEIN
Organism(s): Synechococcus elongatus PCC 7942 = FACHB-805
Expression System: Escherichia coli BL21
Mutation(s): No

Deposited: 2023-06-07 Released: 2024-06-12
Deposition Author(s): Jia, X., Zhang, Q., Li, S., Guo, J.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.51 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

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

Literature

Adaptation of ancient cyanobacterial clock to the day length ~ 0.95 Ga ago

Li, S., Wan, Y.

To be published.

Macromolecule Content

Total Structure Weight: 357.43 kDa
Atom Count: 23,226
Modelled Residue Count: 2,910
Deposited Residue Count: 3,144
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Circadian clock oscillator protein KaiC	A, B, C, D, E A, B, C, D, E, F	524	Synechococcus elongatus PCC 7942 = FACHB-805	Mutation(s): 0 Gene Names: kaiC, Synpcc7942_1216, see0011 EC: 2.7.11.1 (PDB Primary Data), 3.6.4 (PDB Primary Data)
UniProt
Find proteins for Q79PF4 (Synechococcus elongatus (strain ATCC 33912 / PCC 7942 / FACHB-805)) Explore Q79PF4 Go to UniProtKB: Q79PF4
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q79PF4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ATP (Subject of Investigation/LOI) Query on ATP Download Ideal Coordinates CCD File SDF format, chain AA [auth F] SDF format, chain G [auth A] SDF format, chain K [auth B] SDF format, chain O [auth C] SDF format, chain S [auth D] SDF format, chain W [auth E] MOL2 format, chain AA [auth F] MOL2 format, chain G [auth A] MOL2 format, chain K [auth B] MOL2 format, chain O [auth C] MOL2 format, chain S [auth D] MOL2 format, chain W [auth E]	AA [auth F] G [auth A] K [auth B] O [auth C] S [auth D] AA [auth F], G [auth A], K [auth B], O [auth C], S [auth D], W [auth E]	ADENOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₃ P₃ ZKHQWZAMYRWXGA-KQYNXXCUSA-N		Interactions Focus chain AA [auth F] Focus chain G [auth A] Focus chain K [auth B] Focus chain O [auth C] Focus chain S [auth D] Focus chain W [auth E] Interactions & Density Focus chain AA [auth F] Focus chain G [auth A] Focus chain K [auth B] Focus chain O [auth C] Focus chain S [auth D] Focus chain W [auth E]
ADP (Subject of Investigation/LOI) Query on ADP Download Ideal Coordinates CCD File SDF format, chain CA [auth F] SDF format, chain I [auth A] SDF format, chain M [auth B] SDF format, chain Q [auth C] SDF format, chain U [auth D] SDF format, chain Y [auth E] MOL2 format, chain CA [auth F] MOL2 format, chain I [auth A] MOL2 format, chain M [auth B] MOL2 format, chain Q [auth C] MOL2 format, chain U [auth D] MOL2 format, chain Y [auth E]	CA [auth F] I [auth A] M [auth B] Q [auth C] U [auth D] CA [auth F], I [auth A], M [auth B], Q [auth C], U [auth D], Y [auth E]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain CA [auth F] Focus chain I [auth A] Focus chain M [auth B] Focus chain Q [auth C] Focus chain U [auth D] Focus chain Y [auth E] Interactions & Density Focus chain CA [auth F] Focus chain I [auth A] Focus chain M [auth B] Focus chain Q [auth C] Focus chain U [auth D] Focus chain Y [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 F] SDF format, chain H [auth A] SDF format, chain J [auth A] SDF format, chain L [auth B] SDF format, chain N [auth B] SDF format, chain P [auth C] SDF format, chain R [auth C] SDF format, chain T [auth D] SDF format, chain V [auth D] SDF format, chain X [auth E] SDF format, chain Z [auth E] MOL2 format, chain BA [auth F] MOL2 format, chain DA [auth F] MOL2 format, chain H [auth A] MOL2 format, chain J [auth A] MOL2 format, chain L [auth B] MOL2 format, chain N [auth B] MOL2 format, chain P [auth C] MOL2 format, chain R [auth C] MOL2 format, chain T [auth D] MOL2 format, chain V [auth D] MOL2 format, chain X [auth E] MOL2 format, chain Z [auth E]	BA [auth F] DA [auth F] H [auth A] J [auth A] L [auth B] BA [auth F], DA [auth F], H [auth A], J [auth A], L [auth B], N [auth B], P [auth C], R [auth C], T [auth D], V [auth D], X [auth E], Z [auth E]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain BA [auth F] Focus chain DA [auth F] Focus chain H [auth A] Focus chain J [auth A] Focus chain L [auth B] Focus chain N [auth B] Focus chain P [auth C] Focus chain R [auth C] Focus chain T [auth D] Focus chain V [auth D] Focus chain X [auth E] Focus chain Z [auth E] Interactions & Density Focus chain BA [auth F] Focus chain DA [auth F] Focus chain H [auth A] Focus chain J [auth A] Focus chain L [auth B] Focus chain N [auth B] Focus chain P [auth C] Focus chain R [auth C] Focus chain T [auth D] Focus chain V [auth D] Focus chain X [auth E] Focus chain Z [auth E]