8VQK | pdb_00008vqk

YcjN from Escherichia coli


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 
    0.264 (Depositor), 0.260 (DCC) 
  • R-Value Work: 
    0.215 (Depositor), 0.211 (DCC) 
  • R-Value Observed: 
    0.218 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.2 of the entry. See complete history

Literature

Expression, purification, and characterization of diacylated Lipo-YcjN from Escherichia coli.

Trevino, M.A.Amankwah, K.A.Fernandez, D.Weston, S.A.Stewart, C.J.Gallardo, J.M.Shahgholi, M.Sharaf, N.G.

(2024) J Biological Chem 300: 107853-107853

  • DOI: https://doi.org/10.1016/j.jbc.2024.107853
  • Primary Citation Related Structures: 
    8VQK

  • PubMed Abstract: 

    YcjN is a putative substrate binding protein expressed from a cluster of genes involved in carbohydrate import and metabolism in Escherichia coli. Here, we determine the crystal structure of YcjN to a resolution of 1.95 Å, revealing that its three-dimensional structure is similar to substrate binding proteins in subcluster D-I, which includes the well-characterized maltose binding protein (MBP). Furthermore, we found that recombinant overexpression of YcjN results in the formation of a lipidated form of YcjN that is posttranslationally diacylated at cysteine 21. Comparisons of size-exclusion chromatography profiles and dynamic light scattering measurements of lipidated and non-lipidated YcjN proteins suggest that lipidated YcjN aggregates in solution via its lipid moiety. Additionally, bioinformatic analysis indicates that YcjN-like proteins may exist in both Bacteria and Archaea, potentially in both lipidated and non-lipidated forms. Together, our results provide a better understanding of the aggregation properties of recombinantly expressed bacterial lipoproteins in solution and establish a foundation for future studies that aim to elucidate the role of these proteins in bacterial physiology.


  • Organizational Affiliation
    • Department of Biology, Stanford University, Stanford CA 94305.

Macromolecule Content 

  • Total Structure Weight: 97.45 kDa 
  • Atom Count: 6,501 
  • Modeled Residue Count: 803 
  • Deposited Residue Count: 880 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Putative ABC transporter periplasmic-binding protein YcjN
A, B
440Escherichia coliMutation(s): 0 
Gene Names: ycjNb1310JW1303
UniProt
Find proteins for P76042 (Escherichia coli (strain K12))
Explore P76042 
Go to UniProtKB:  P76042
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP76042
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CD

Query on CD



Download:Ideal Coordinates CCD File
I [auth B],
J [auth B]
CADMIUM ION
Cd
WLZRMCYVCSSEQC-UHFFFAOYSA-N
PEG

Query on PEG



Download:Ideal Coordinates CCD File
E [auth A],
K [auth B],
L [auth B]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
SO4

Query on SO4



Download:Ideal Coordinates CCD File
C [auth A],
H [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL

Query on GOL



Download:Ideal Coordinates CCD File
D [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
K

Query on K



Download:Ideal Coordinates CCD File
F [auth A],
G [auth A],
M [auth B],
N [auth B]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free:  0.264 (Depositor), 0.260 (DCC) 
  • R-Value Work:  0.215 (Depositor), 0.211 (DCC) 
  • R-Value Observed: 0.218 (Depositor) 
Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 63.216α = 110.01
b = 63.29β = 91.09
c = 74.314γ = 118.66
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2024-10-09
    Type: Initial release
  • Version 1.1: 2024-10-16
    Changes: Database references
  • Version 1.2: 2024-11-13
    Changes: Database references