5FVN | pdb_00005fvn

X-ray crystal structure of Enterobacter cloacae OmpE36 porin.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 
    0.183 (Depositor), 0.199 (DCC) 
  • R-Value Work: 
    0.155 (Depositor) 
  • R-Value Observed: 
    0.156 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 4.2 of the entry. See complete history

Literature

Gram-negative trimeric porins have specific LPS binding sites that are essential for porin biogenesis.

Arunmanee, W.Pathania, M.Solovyova, A.S.Le Brun, A.P.Ridley, H.Basle, A.van den Berg, B.Lakey, J.H.

(2016) Proc Natl Acad Sci U S A 113: E5034-E5043

  • DOI: https://doi.org/10.1073/pnas.1602382113
  • Primary Citation Related Structures: 
    5FVN

  • PubMed Abstract: 

    The outer membrane (OM) of gram-negative bacteria is an unusual asymmetric bilayer with an external monolayer of lipopolysaccharide (LPS) and an inner layer of phospholipids. The LPS layer is rigid and stabilized by divalent cation cross-links between phosphate groups on the core oligosaccharide regions. This means that the OM is robust and highly impermeable to toxins and antibiotics. During their biogenesis, OM proteins (OMPs), which function as transporters and receptors, must integrate into this ordered monolayer while preserving its impermeability. Here we reveal the specific interactions between the trimeric porins of Enterobacteriaceae and LPS. Isolated porins form complexes with variable numbers of LPS molecules, which are stabilized by calcium ions. In earlier studies, two high-affinity sites were predicted to contain groups of positively charged side chains. Mutation of these residues led to the loss of LPS binding and, in one site, also prevented trimerization of the porin, explaining the previously observed effect of LPS mutants on porin folding. The high-resolution X-ray crystal structure of a trimeric porin-LPS complex not only helps to explain the mutagenesis results but also reveals more complex, subtle porin-LPS interactions and a bridging calcium ion.


  • Organizational Affiliation
    • Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE2 4HH, United Kingdom;

Macromolecule Content 

  • Total Structure Weight: 262.36 kDa 
  • Atom Count: 19,668 
  • Modeled Residue Count: 2,052 
  • Deposited Residue Count: 2,052 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
OMPC PORIN
A, B, C, D, E
A, B, C, D, E, F
342Enterobacter cloacaeMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q93K99 (Enterobacter cloacae)
Explore Q93K99 
Go to UniProtKB:  Q93K99
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ93K99
Sequence Annotations
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Reference Sequence

Oligosaccharides

Help  
Entity ID: 2
MoleculeChains Length2D Diagram GlycosylationD Interactions
3-deoxy-alpha-D-manno-oct-2-ulopyranosonic acid-(2-6)-2-amino-2-deoxy-4-O-phosphono-beta-D-glucopyranose-(1-6)-2-amino-2-deoxy-1-O-phosphono-alpha-D-glucopyranose
G, K, L, M
3N/A
Entity ID: 3
MoleculeChains Length2D Diagram GlycosylationD Interactions
3-deoxy-alpha-D-manno-oct-2-ulopyranosonic acid-(2-4)-[L-glycero-alpha-D-manno-heptopyranose-(1-5)]3-deoxy-alpha-D-manno-oct-2-ulopyranosonic acid-(2-6)-2-amino-2-deoxy-4-O-phosphono-beta-D-glucopyranose-(1-6)-2-amino-2-deoxy-1-O-phosphono-alpha-D-glucopyranose
H, I, N
5N/A
Entity ID: 4
MoleculeChains Length2D Diagram GlycosylationD Interactions
3-deoxy-alpha-D-manno-oct-2-ulopyranosonic acid-(2-4)-3-deoxy-alpha-D-manno-oct-2-ulopyranosonic acid-(2-6)-2-amino-2-deoxy-4-O-phosphono-beta-D-glucopyranose-(1-6)-2-amino-2-deoxy-1-O-phosphono-alpha-D-glucopyranose
J, O
4N/A

Small Molecules

Ligands 8 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
C8E

Query on C8E



Download:Ideal Coordinates CCD File
AB [auth C]
AC [auth D]
BB [auth C]
BC [auth D]
CB [auth C]
AB [auth C],
AC [auth D],
BB [auth C],
BC [auth D],
CB [auth C],
CC [auth D],
DB [auth C],
DC [auth D],
DD [auth F],
ED [auth F],
FD [auth F],
IA [auth B],
JA [auth B],
KA [auth B],
LA [auth B],
MA [auth B],
Q [auth A],
R [auth A],
S [auth A],
T [auth A],
TC [auth E],
U [auth A],
UA [auth C],
V [auth A],
VA [auth C],
VB [auth D],
W [auth A],
WA [auth C],
WB [auth D],
X [auth A],
XA [auth C],
XB [auth D],
Y [auth A],
YA [auth C],
YB [auth D],
ZA [auth C],
ZB [auth D]
(HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE
C16 H34 O5
FEOZZFHAVXYAMB-UHFFFAOYSA-N
FTT

Query on FTT



Download:Ideal Coordinates CCD File
AD [auth E]
BA [auth A]
CA [auth A]
DA [auth A]
GA [auth A]
AD [auth E],
BA [auth A],
CA [auth A],
DA [auth A],
GA [auth A],
GB [auth C],
HC [auth D],
IB [auth C],
IC [auth D],
ID [auth F],
JB [auth C],
JC [auth D],
JD [auth F],
KB [auth C],
KC [auth D],
KD [auth F],
LB [auth C],
LD [auth F],
MD [auth F],
NC [auth D],
OA [auth B],
OC [auth D],
PA [auth B],
PB [auth C],
PC [auth D],
QA [auth B],
QB [auth C],
QD [auth F],
RA [auth B],
RB [auth C],
RD [auth F],
SC [auth D],
SD [auth F],
WC [auth E],
YC [auth E],
ZC [auth E]
3-HYDROXY-TETRADECANOIC ACID
C14 H28 O3
ATRNZOYKSNPPBF-CYBMUJFWSA-N
KDO

Query on KDO



Download:Ideal Coordinates CCD File
AA [auth A],
GC [auth D],
VC [auth E]
3-deoxy-alpha-D-manno-oct-2-ulopyranosonic acid
C8 H14 O8
NNLZBVFSCVTSLA-HXUQBWEZSA-N
MYR

Query on MYR



Download:Ideal Coordinates CCD File
BD [auth E]
EA [auth A]
MB [auth C]
MC [auth D]
ND [auth F]
BD [auth E],
EA [auth A],
MB [auth C],
MC [auth D],
ND [auth F],
QC [auth D],
SA [auth B],
SB [auth C],
TD [auth F]
MYRISTIC ACID
C14 H28 O2
TUNFSRHWOTWDNC-UHFFFAOYSA-N
DAO

Query on DAO



Download:Ideal Coordinates CCD File
CD [auth E]
FA [auth A]
FC [auth D]
HA [auth A]
HB [auth C]
CD [auth E],
FA [auth A],
FC [auth D],
HA [auth A],
HB [auth C],
LC [auth D],
NB [auth C],
OB [auth C],
OD [auth F],
PD [auth F],
RC [auth D],
TA [auth B],
TB [auth C],
UD [auth F],
XC [auth E]
LAURIC ACID
C12 H24 O2
POULHZVOKOAJMA-UHFFFAOYSA-N
SO4

Query on SO4



Download:Ideal Coordinates CCD File
P [auth A],
UB [auth D]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
PO4

Query on PO4



Download:Ideal Coordinates CCD File
EB [auth C]
EC [auth D]
GD [auth F]
NA [auth B]
UC [auth E]
EB [auth C],
EC [auth D],
GD [auth F],
NA [auth B],
UC [auth E],
Z [auth A]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
CA

Query on CA



Download:Ideal Coordinates CCD File
FB [auth C],
HD [auth F]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free:  0.183 (Depositor), 0.199 (DCC) 
  • R-Value Work:  0.155 (Depositor) 
  • R-Value Observed: 0.156 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 109.749α = 90
b = 123.26β = 91.01
c = 116.01γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-08-10
    Type: Initial release
  • Version 1.1: 2016-08-17
    Changes: Database references
  • Version 1.2: 2016-09-28
    Changes: Database references
  • Version 1.3: 2018-02-21
    Changes: Advisory, Database references, Structure summary
  • Version 2.0: 2019-01-30
    Changes: Advisory, Atomic model, Data collection, Derived calculations
  • Version 3.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Non-polymer description, Other, Structure summary
  • Version 4.0: 2022-04-20
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Structure summary
  • Version 4.1: 2023-03-08
    Changes: Structure summary
  • Version 4.2: 2024-02-07
    Changes: Data collection, Refinement description