3D3Q | pdb_00003d3q

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)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free:
0.271 (Depositor), 0.282 (DCC)
R-Value Work:
0.231 (Depositor), 0.244 (DCC)
R-Value Observed:
0.231 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

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.

Macromolecule Content

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

Macromolecules

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| 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8CQL3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on 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 (Depositor), 0.282 (DCC)
R-Value Work: 0.231 (Depositor), 0.244 (DCC)
R-Value Observed: 0.231 (Depositor)

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

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2008-07-15

Deposition Author(s):

Northeast Structural Genomics Consortium (NESG)

Revision History (Full details and data files)

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