4O0M | pdb_00004o0m

Crystal structure of T. Elongatus BP-1 Clock Protein KaiC

PDB DOI: https://doi.org/10.2210/pdb4O0M/pdb

Classification: TRANSFERASE
Organism(s): Thermosynechococcus vestitus BP-1
Expression System: Escherichia coli BL21
Mutation(s): No

Deposited: 2013-12-13 Released: 2014-05-14
Deposition Author(s): Pattanayek, R., Egli, M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.84 Å
R-Value Free:
0.270 (Depositor), 0.266 (DCC)
R-Value Work:
0.225 (Depositor), 0.226 (DCC)
R-Value Observed:
0.227 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

An arginine tetrad as mediator of input-dependent and input-independent ATPases in the clock protein KaiC

Pattanayek, R., Xu, Y., Lamichhane, A., Johnson, C.H., Egli, M.

(2014) Acta Crystallogr D Biol Crystallogr D70: 1375-1390

Macromolecule Content

Total Structure Weight: 178.96 kDa
Atom Count: 11,943
Modeled Residue Count: 1,474
Deposited Residue Count: 1,572
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Circadian clock protein kinase KaiC	A, B, C	524	Thermosynechococcus vestitus BP-1	Mutation(s): 0 Gene Names: kaiC, tlr0483 EC: 2.7.11.1 (PDB Primary Data), 3.6.4 (UniProt)
UniProt
Find proteins for Q79V60 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1)) Explore Q79V60 Go to UniProtKB: Q79V60
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q79V60
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ATP Query on ATP Download:Ideal Coordinates CCD File SDF format, chain N [auth C] SDF format, chain M [auth C] SDF format, chain K [auth B] SDF format, chain I [auth B] SDF format, chain F [auth A] SDF format, chain E [auth A] MOL2 format, chain N [auth C] MOL2 format, chain M [auth C] MOL2 format, chain K [auth B] MOL2 format, chain I [auth B] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] mmCIF format, chain N [auth C] mmCIF format, chain M [auth C] mmCIF format, chain K [auth B] mmCIF format, chain I [auth B] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A]	E [auth A] F [auth A] I [auth B] K [auth B] M [auth C] E [auth A], F [auth A], I [auth B], K [auth B], M [auth C], N [auth C]	ADENOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₃ P₃ ZKHQWZAMYRWXGA-KQYNXXCUSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain I [auth B] Focus chain K [auth B] Focus chain M [auth C] Focus chain N [auth C] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain I [auth B] Focus chain K [auth B] Focus chain M [auth C] Focus chain N [auth C]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain O [auth C] SDF format, chain L [auth C] SDF format, chain J [auth B] SDF format, chain H [auth B] SDF format, chain G [auth A] SDF format, chain D [auth A] MOL2 format, chain O [auth C] MOL2 format, chain L [auth C] MOL2 format, chain J [auth B] MOL2 format, chain H [auth B] MOL2 format, chain G [auth A] MOL2 format, chain D [auth A] mmCIF format, chain O [auth C] mmCIF format, chain L [auth C] mmCIF format, chain J [auth B] mmCIF format, chain H [auth B] mmCIF format, chain G [auth A] mmCIF format, chain D [auth A]	D [auth A] G [auth A] H [auth B] J [auth B] L [auth C] D [auth A], G [auth A], H [auth B], J [auth B], L [auth C], O [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain G [auth A] Focus chain H [auth B] Focus chain J [auth B] Focus chain L [auth C] Focus chain O [auth C] Interactions & Density Focus chain D [auth A] Focus chain G [auth A] Focus chain H [auth B] Focus chain J [auth B] Focus chain L [auth C] Focus chain O [auth C]

Modified Residues 2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
SEP Query on SEP	A, B, C	L-PEPTIDE LINKING	C₃ H₈ N O₆ P		SER
TPO Query on TPO	A, B, C	L-PEPTIDE LINKING	C₄ H₁₀ N O₆ P		THR

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.84 Å
R-Value Free: 0.270 (Depositor), 0.266 (DCC)
R-Value Work: 0.225 (Depositor), 0.226 (DCC)
R-Value Observed: 0.227 (Depositor)

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 130.81	α = 90
b = 195.29	β = 90
c = 136.64	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHASER	phasing
PHENIX	refinement
HKL-2000	data reduction
XSCALE	data scaling

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2014-05-14

Deposition Author(s):

Pattanayek, R.

Egli, M.

Revision History (Full details and data files)

Version 1.0: 2014-05-14
Type: Initial release
Version 1.1: 2024-10-30
Changes: Data collection, Database references, Derived calculations, Structure summary

4O0M | pdb_00004o0m

Crystal structure of T. Elongatus BP-1 Clock Protein KaiC

Literature

An arginine tetrad as mediator of input-dependent and input-independent ATPases in the clock protein KaiC

Biological Assembly 1

Macromolecules

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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