3MPD | pdb_00003mpd

Crystal structure of nucleoside diphosphate kinase from encephalitozoon cuniculi, cubic form, apo

• PDB DOI: https://doi.org/10.2210/pdb3MPD/pdb

• Classification: TRANSFERASE
• Organism(s): Encephalitozoon cuniculi
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2010-04-26 Released: 2010-05-12 
• Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.08 Å
• R-Value Free: 
  0.207 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.175 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.177 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of nucleoside diphosphate kinase from encephalitozoon cuniculi

Gardberg, A., Edwards, T.E., Staker, B., SSGCID

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly 2  

Global Symmetry: Dihedral - D3  (Explore in 3D)
Global Stoichiometry: Homo 6-mer - A6 

Biological assembly 2 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 34.02 kDa 
• Atom Count: 2,566 
• Modeled Residue Count: 294 
• Deposited Residue Count: 302 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nucleoside diphosphate kinase	A, B	151	Encephalitozoon cuniculi	Mutation(s): 0  Gene Names: ECU06_1530, HM-1:IMSS, NDK1 EC: 2.7.4.6
UniProt
Find proteins for Q8SRM7 (Encephalitozoon cuniculi (strain GB-M1)) Explore Q8SRM7  Go to UniProtKB:  Q8SRM7

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	C [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.08 Å
• R-Value Free:  0.207 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.175 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.177 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M33MPD

Space Group: P 2₁ 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 111.33	α = 90
b = 111.33	β = 90
c = 111.33	γ = 90

Software Package:

Software Name	Purpose
Blu-Ice	data collection
PHASER	phasing
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-05-12 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History  

• Version 1.0: 2010-05-12
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-09-06
  Changes: Data collection, Database references, Derived calculations, Refinement description