1ION

THE SEPTUM SITE-DETERMINING PROTEIN MIND COMPLEXED WITH MG-ADP FROM PYROCOCCUS HORIKOSHII OT3

• PDB DOI: https://doi.org/10.2210/pdb1ION/pdb

• Classification: CELL CYCLE
• Organism(s): Pyrococcus horikoshii OT3
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2001-03-21 Released: 2001-09-26 
• Deposition Author(s): Sakai, N., Yao, M., Itou, H., Watanabe, N., Yumoto, F., Tanokura, M., Tanaka, I.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.188 
• R-Value Work: 0.228 
• R-Value Observed: 0.228 

Literature

The three-dimensional structure of septum site-determining protein MinD from Pyrococcus horikoshii OT3 in complex with Mg-ADP.

Sakai, N., Yao, M., Itou, H., Watanabe, N., Yumoto, F., Tanokura, M., Tanaka, I.

(2001) Structure 9: 817-826

• PubMed: 11566131 
• DOI: https://doi.org/10.1016/s0969-2126(01)00638-4
• Primary Citation of Related Structures:  
  1ION


• PubMed Abstract: 
  

  In Escherichia coli, the cell division site is determined by the cooperative activity of min operon products MinC, MinD, and MinE. MinC is a nonspecific inhibitor of the septum protein FtsZ, and MinE is the supressor of MinC. MinD plays a multifunctional role. It is a membrane-associated ATPase and is a septum site-determining factor through the activation and regulation of MinC and MinE. MinD is also known to undergo a rapid pole-to-pole oscillation movement in vivo as observed by fluorescent microscopy.

---

Organizational Affiliation: 

Division of Biological Sciences, Graduate School of Science, Hokkaido University, Sapporo 060-0810, Japan.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 26.96 kDa 
• Atom Count: 1,887 
• Modelled Residue Count: 243 
• Deposited Residue Count: 243 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PROBABLE CELL DIVISION INHIBITOR MIND	A	243	Pyrococcus horikoshii OT3	Mutation(s): 9  Gene Names: MIND-2
UniProt
Find proteins for O58346 (Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3)) Explore O58346  Go to UniProtKB:  O58346

Small Molecules

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

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.188 
• R-Value Work: 0.228 
• R-Value Observed: 0.228 
• Space Group: P 2₁ 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 96.59	α = 90
b = 96.59	β = 90
c = 96.59	γ = 90

Software Package:

Software Name	Purpose
SHARP	phasing
SOLVE	phasing
CNS	refinement
MOSFLM	data reduction
CCP4	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2001-09-26 
Deposition Author(s): Sakai, N., Yao, M., Itou, H., Watanabe, N., Yumoto, F., Tanokura, M., Tanaka, I.

Revision History  

• Version 1.0: 2001-09-26
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Source and taxonomy, Version format compliance
• Version 1.3: 2023-12-27
  Changes: Data collection, Database references, Derived calculations