3MKD | pdb_00003mkd

Crystal structure of myosin-2 dictyostelium discoideum motor domain S456Y mutant in complex with adp-orthovanadate

• PDB DOI: https://doi.org/10.2210/pdb3MKD/pdb

• Classification: CONTRACTILE PROTEIN
• Organism(s): Dictyostelium discoideum
• Expression System: Dictyostelium discoideum
• Mutation(s): Yes 


• Deposited: 2010-04-14 Released: 2011-04-06 
• Deposition Author(s): Kathmann, D., Diensthuber, R.P., Fedorov, R., Manstein, D.J., Tsiavaliaris, G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 
  0.240 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.199 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.200 (Depositor) 

Starting Model: experimental

Literature

Switch-2 dependent modulation of the myosin power stroke

Kathmann, D., Diensthuber, R.P., Fedorov, R., Manstein, D.J., Tsiavaliaris, G.

To be published.

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 79.26 kDa 
• Atom Count: 5,902 
• Modeled Residue Count: 692 
• Deposited Residue Count: 692 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Myosin-2 heavy chain	A	692	Dictyostelium discoideum	Mutation(s): 1  EC: 3.6.4.1
UniProt
Find proteins for P08799 (Dictyostelium discoideum) Explore P08799  Go to UniProtKB:  P08799

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ADP	D [auth A]	ADENOSINE-5'-DIPHOSPHATE C10 H15 N5 O10 P2 XTWYTFMLZFPYCI-KQYNXXCUSA-N
VO4	C [auth A]	VANADATE ION O4 V LSGOVYNHVSXFFJ-UHFFFAOYSA-N
MG	B [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free:  0.240 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.199 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.200 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 89.601	α = 90
b = 147.356	β = 90
c = 153.899	γ = 90

Software Package:

Software Name	Purpose
MxCuBE	data collection
AMoRE	phasing
CNS	refinement
XDS	data reduction
XSCALE	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-04-06 
Deposition Author(s): Kathmann, D., Diensthuber, R.P., Fedorov, R., Manstein, D.J., Tsiavaliaris, G.

Revision History  

• Version 1.0: 2011-04-06
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-11-01
  Changes: Data collection, Database references, Derived calculations, Refinement description