2ZTS | pdb_00002zts

Crystal structure of KaiC-like protein PH0186 from hyperthermophilic archaea Pyrococcus horikoshii OT3

• PDB DOI: https://doi.org/10.2210/pdb2ZTS/pdb

• Classification: ATP-binding protein
• Organism(s): Pyrococcus horikoshii
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-10-08 Released: 2009-03-24 
• Deposition Author(s): Ming, H., Miyazono, K., Tanokura, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.07 Å
• R-Value Free: 
  0.250 (Depositor) 
• R-Value Work: 
  0.197 (Depositor), 0.211 (DCC) 
• R-Value Observed: 
  0.199 (Depositor) 

Literature

Crystal structure of KaiC-like protein PH0186 from hyperthermophilic archaea Pyrococcus horikoshii OT3.

Kang, H.-J., Kubota, K., Ming, H., Miyazono, K., Tanokura, M.

(2009) Proteins 75: 1035-1039

• PubMed: 19274727 
• DOI: https://doi.org/10.1002/prot.22367
• Primary Citation Related Structures: 
  2ZTS

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Organizational Affiliation: 
• Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan.

Biological Assembly 1  

Global Symmetry: Cyclic - C6  (Explore in 3D)
Global Stoichiometry: Homo 6-mer - A6 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 87.99 kDa 
• Atom Count: 5,442 
• Modeled Residue Count: 658 
• Deposited Residue Count: 753 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative uncharacterized protein PH0186	A, B, C	251	Pyrococcus horikoshii	Mutation(s): 0
UniProt
Find proteins for O57925 (Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3)) Explore O57925  Go to UniProtKB:  O57925

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ADP	D [auth A], F [auth B], H [auth C]	ADENOSINE-5'-DIPHOSPHATE C10 H15 N5 O10 P2 XTWYTFMLZFPYCI-KQYNXXCUSA-N
MG	E [auth A], G [auth B], I [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B, C	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.07 Å
• R-Value Free:  0.250 (Depositor) 
• R-Value Work:  0.197 (Depositor), 0.211 (DCC) 
• R-Value Observed: 0.199 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 173.655	α = 90
b = 51.807	β = 122.83
c = 97.468	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
SOLVE	phasing
RESOLVE	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
HKL-2000	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-03-24 
Deposition Author(s): Ming, H., Miyazono, K., Tanokura, M.

Revision History  

• Version 1.0: 2009-03-24
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-10-11
  Changes: Refinement description
• Version 1.3: 2024-10-30
  Changes: Data collection, Database references, Derived calculations, Structure summary
• Version 1.4: 2025-04-30
  Changes: Database references
• Version 1.5: 2025-07-02
  Changes: Structure summary