4YS8

Crystal Structure of 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase (IspD) from Burkholderia thailandensis

• PDB DOI: https://doi.org/10.2210/pdb4YS8/pdb

• Classification: TRANSFERASE
• Organism(s): Burkholderia thailandensis E264
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2015-03-16 Released: 2015-04-01 
• Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.45 Å
• R-Value Free: 0.263 
• R-Value Work: 0.216 
• R-Value Observed: 0.218 

Starting Model: experimental

Literature

Crystal Structure of 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase (IspD) from Burkholderia thailandensis

Dranow, D.M., Fairman, J.W., Pierce, P.G., Lorimer, D., Edwards, T.E., SSGCID

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

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.

Biological Assembly 5  

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

Biological assembly 5 generated by PISA (software)

Biological Assembly 6  

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

Biological assembly 6 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 103.81 kDa 
• Atom Count: 6,897 
• Modelled Residue Count: 887 
• Deposited Residue Count: 964 
• 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	241	Burkholderia thailandensis E264	Mutation(s): 0  Gene Names: ispD, BTH_I2089 EC: 2.7.7.60
UniProt
Find proteins for Q2SWT6 (Burkholderia thailandensis (strain ATCC 700388 / DSM 13276 / CCUG 48851 / CIP 106301 / E264)) Explore Q2SWT6  Go to UniProtKB:  Q2SWT6

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	E [auth A], F [auth A], G [auth B], I [auth C], J [auth C]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ACT	H [auth B]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.45 Å
• R-Value Free: 0.263 
• R-Value Work: 0.216 
• R-Value Observed: 0.218 
• Space Group: P 1 2₁ 1
• Diffraction Data: https://doi.org/10.18430/M34YS8

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.65	α = 90
b = 138.31	β = 101.89
c = 78.59	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
MR-Rosetta	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-04-01 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History  

• Version 1.0: 2015-04-01
  Type: Initial release
  
• Version 1.1: 2015-04-08
  Changes: Other
• Version 1.2: 2015-10-28
  Changes: Database references
• Version 1.3: 2017-10-11
  Changes: Data collection, Derived calculations
• Version 1.4: 2021-11-03
  Changes: Data collection, Database references
• Version 1.5: 2023-09-27
  Changes: Data collection, Refinement description