5F15

Crystal Structure of ArnT from Cupriavidus metallidurans bound to Undecaprenyl phosphate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.2 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.222 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structures of aminoarabinose transferase ArnT suggest a molecular basis for lipid A glycosylation.

Petrou, V.I.Herrera, C.M.Schultz, K.M.Clarke, O.B.Vendome, J.Tomasek, D.Banerjee, S.Rajashankar, K.R.Belcher Dufrisne, M.Kloss, B.Kloppmann, E.Rost, B.Klug, C.S.Trent, M.S.Shapiro, L.Mancia, F.

(2016) Science 351: 608-612


Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
4-amino-4-deoxy-L-arabinose (L-Ara4N) transferase
A
578Cupriavidus metallidurans (strain ATCC 43123 / DSM 2839 / NBRC 102507 / CH34)Mutation(s): 0 
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Glycosyltransfereases
Protein: 
ArnT glycosyltransferase, apo form
Find proteins for Q1LDT6 (Cupriavidus metallidurans (strain ATCC 43123 / DSM 2839 / NBRC 102507 / CH34))
Go to UniProtKB:  Q1LDT6
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EPE
Query on EPE

Download SDF File 
Download CCD File 
A
4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
HEPES
C8 H18 N2 O4 S
JKMHFZQWWAIEOD-UHFFFAOYSA-N
 Ligand Interaction
PO4
Query on PO4

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Download CCD File 
A
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
5TR
Query on 5TR

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Download CCD File 
A
[(2~{E},6~{E},10~{E},14~{E},18~{Z},22~{E},26~{Z},30~{E},34~{E},38~{E})-3,7,11,15,19,23,27,31,35,39,43-undecamethyltetratetraconta-2,6,10,14,18,22,26,30,34,38,42-undecaenyl] dihydrogen phosphate
Undecaprenyl phosphate
C55 H91 O4 P
UFPHFKCTOZIAFY-ZUPWODLNSA-N
 Ligand Interaction
CL
Query on CL

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Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
MPG
Query on MPG

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Download CCD File 
A
[(Z)-octadec-9-enyl] (2R)-2,3-bis(oxidanyl)propanoate
C21 H40 O4
JPJYKWFFJCWMPK-GDCKJWNLSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.2 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.222 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 59.648α = 90.00
b = 80.322β = 90.00
c = 150.161γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
Cootmodel building
Aimlessdata scaling
XDSdata reduction
PDB_EXTRACTdata extraction
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical SciencesUnited StatesU54 GM095315
National Institutes of Health/National Institute of General Medical SciencesUnited StatesR01 GM111980

Revision History 

  • Version 1.0: 2016-02-17
    Type: Initial release
  • Version 1.1: 2017-09-13
    Type: Author supporting evidence, Database references, Derived calculations
  • Version 1.2: 2018-04-18
    Type: Data collection, Database references