3D3Q

Crystal structure of tRNA delta(2)-isopentenylpyrophosphate transferase (SE0981) from Staphylococcus epidermidis. Northeast Structural Genomics Consortium target SeR100

• PDB DOI: https://doi.org/10.2210/pdb3D3Q/pdb

• Classification: TRANSFERASE
• Organism(s): Staphylococcus epidermidis ATCC 12228
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-05-12 Released: 2008-07-15 
• Deposition Author(s): Forouhar, F., Abashidze, M., Seetharaman, J., Mao, L., Xiao, R., Maglaqui, M., Lee, D., Everett, J.K., Acton, T.B., Montelione, G.T., Tong, L., Hunt, J.F., Northeast Structural Genomics Consortium (NESG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.271 
• R-Value Work: 0.231 
• R-Value Observed: 0.231 

Literature

Crystal structure of tRNA delta(2)-isopentenylpyrophosphate transferase (SE0981) from Staphylococcus epidermidis.

Forouhar, F., Abashidze, M., Seetharaman, J., Mao, L., Xiao, R., Maglaqui, M., Lee, D., Everett, J.K., Acton, T.B., Montelione, G.T., Tong, L., Hunt, J.F.

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)

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 80.73 kDa 
• Atom Count: 5,011 
• Modelled Residue Count: 610 
• Deposited Residue Count: 680 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
tRNA delta(2)-isopentenylpyrophosphate transferase	A, B	340	Staphylococcus epidermidis ATCC 12228	Mutation(s): 0  Gene Names: miaA, SE_0981 EC: 2.5.1.8 (PDB Primary Data), 2.5.1.75 (UniProt)
UniProt
Find proteins for Q8CQL3 (Staphylococcus epidermidis (strain ATCC 12228 / FDA PCI 1200)) Explore Q8CQL3  Go to UniProtKB:  Q8CQL3

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.271 
• R-Value Work: 0.231 
• R-Value Observed: 0.231 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.622	α = 90
b = 84.48	β = 102.87
c = 75.397	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
ADSC	data collection
DENZO	data reduction
SCALEPACK	data scaling
SnB	phasing
RESOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-07-15 
Deposition Author(s): Forouhar, F., Abashidze, M., Seetharaman, J., Mao, L., Xiao, R., Maglaqui, M., Lee, D., Everett, J.K., Acton, T.B., Montelione, G.T., Tong, L., Hunt, J.F., Northeast Structural Genomics Consortium (NESG)

Revision History  

• Version 1.0: 2008-07-15
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-10-25
  Changes: Refinement description
• Version 1.3: 2024-11-20
  Changes: Data collection, Database references, Derived calculations, Structure summary