7KMW

Crystal structure of IspD from Mycobacterium paratuberculosis

• PDB DOI: https://doi.org/10.2210/pdb7KMW/pdb

• Classification: TRANSFERASE
• Organism(s): Mycobacterium avium subsp. paratuberculosis K-10
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2020-11-03 Released: 2020-11-11 
• Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free: 0.223 
• R-Value Work: 0.180 
• R-Value Observed: 0.183 

Literature

Crystal structure of IspD from Mycobacterium paratuberculosis

Pierce, P.G., Bolejack, M.J., Yano, J.K., Lorimer, D.D., Horanyi, P.S., Edwards, T.E.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Biological Assembly 3  

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

Biological assembly 3 assigned by authors.

Biological Assembly 4  

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

Biological assembly 4 assigned by authors.

Macromolecule Content

• Total Structure Weight: 105.64 kDa 
• Atom Count: 6,309 
• Modelled Residue Count: 856 
• Deposited Residue Count: 1,028 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase	A, B, C, D	257	Mycobacterium avium subsp. paratuberculosis K-10	Mutation(s): 0  Gene Names: ispD, MAP_0476 EC: 2.7.7.60
UniProt
Find proteins for Q743W5 (Mycolicibacterium paratuberculosis (strain ATCC BAA-968 / K-10)) Explore Q743W5  Go to UniProtKB:  Q743W5

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	E [auth A], F [auth A], G [auth A], H [auth A], I [auth B], J [auth C], K [auth C], L [auth C], M [auth C], N [auth D], O [auth D], P [auth D]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free: 0.223 
• R-Value Work: 0.180 
• R-Value Observed: 0.183 
• Space Group: C 1 2 1
• Diffraction Data: https://doi.org/10.18430/m37kmw

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 194.13	α = 90
b = 45.62	β = 126.75
c = 121.56	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
XSCALE	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
MoRDa	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-11-11 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History  

• Version 1.0: 2020-11-11
  Type: Initial release
  
• Version 1.1: 2021-07-21
  Changes: Other, Structure summary
• Version 1.2: 2023-10-18
  Changes: Data collection, Database references, Refinement description