2WQT | pdb_00002wqt

Dodecahedral assembly of MhpD


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 
    0.234 (Depositor), 0.231 (DCC) 
  • R-Value Work: 
    0.222 (Depositor), 0.220 (DCC) 
  • R-Value Observed: 
    0.223 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 2WQT

This is version 1.3 of the entry. See complete history

Literature

Assembly of a 20Nm Protein Cage by Escherichia Coli 2-Hydroxypentadienoic Acid Hydratase (Mhpd).

Montgomery, M.G.Coker, A.R.Taylor, I.A.Wood, S.P.

(2010) J Mol Biology 396: 1379

  • DOI: https://doi.org/10.1016/j.jmb.2009.12.056
  • Primary Citation Related Structures: 
    2WQT

  • PubMed Abstract: 

    The pentameric Escherichia coli enzyme 2-hydroxypentadienoic acid hydratase assembles to form a 20-nm-diameter particle comprising 60 protein subunits, arranged with 532 symmetry when crystallised at low pH in the presence of phosphate or sulphate ions. The particles form rapidly and are stable in solution during gel filtration at low pH. They are probably formed through trimers of pentamers, which are stabilised by the interaction of two phosphate ions with residues of the N-terminal domains of subunits at the 3-fold axis. Once the particles are formed at high concentrations of phosphate (or sulphate), they remain stable in solution at 20-fold lower concentrations of the anion. Guest molecules can be trapped within the hollow protein shell during assembly. The C-termini of the subunits are freely accessible on the surface of the protein cage and thus are ideal sites for addition of affinity tags or other modifications. These particles offer a convenient model system for studying the assembly of large symmetrical structures and a novel protein nanoparticle for encapsulation and cargo delivery.


  • Organizational Affiliation
    • Division of Medicine, UCL Medical School, Centre for Amyloidosis and Acute Phase Proteins, London NW3 2PF, UK. mark.montgomery@ucl.ac.uk

Macromolecule Content 

  • Total Structure Weight: 585.51 kDa 
  • Atom Count: 40,183 
  • Modeled Residue Count: 5,240 
  • Deposited Residue Count: 5,400 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
2-KETO-4-PENTENOATE HYDRATASE
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T
270Escherichia coli K-12Mutation(s): 0 
EC: 4.2.1.80
UniProt
Find proteins for P77608 (Escherichia coli (strain K12))
Explore P77608 
Go to UniProtKB:  P77608
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP77608
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PO4

Query on PO4



Download:Ideal Coordinates CCD File
AA [auth B]
AB [auth H]
AC [auth P]
BA [auth B]
BB [auth I]
AA [auth B],
AB [auth H],
AC [auth P],
BA [auth B],
BB [auth I],
BC [auth P],
DA [auth C],
EB [auth J],
EC [auth Q],
FB [auth J],
FC [auth Q],
GA [auth D],
GB [auth K],
GC [auth Q],
HA [auth D],
HB [auth K],
IA [auth D],
IB [auth K],
KC [auth R],
LA [auth E],
LB [auth L],
MB [auth L],
NC [auth S],
OA [auth F],
PA [auth F],
QA [auth F],
RB [auth M],
RC [auth T],
TA [auth G],
TB [auth N],
U [auth A],
UA [auth G],
V [auth A],
VA [auth G],
W [auth A],
WB [auth O],
ZA [auth H],
ZB [auth P]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
K

Query on K



Download:Ideal Coordinates CCD File
CA [auth B]
CB [auth I]
CC [auth P]
EA [auth C]
IC [auth Q]
CA [auth B],
CB [auth I],
CC [auth P],
EA [auth C],
IC [auth Q],
JA [auth D],
JB [auth K],
JC [auth Q],
LC [auth R],
MA [auth E],
NB [auth L],
QB [auth L],
QC [auth S],
RA [auth F],
SC [auth T],
UB [auth N],
WA [auth G],
Y [auth A],
YA [auth G],
Z [auth A]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
NA

Query on NA



Download:Ideal Coordinates CCD File
DB [auth I]
DC [auth P]
FA [auth C]
HC [auth Q]
KA [auth D]
DB [auth I],
DC [auth P],
FA [auth C],
HC [auth Q],
KA [auth D],
KB [auth K],
MC [auth R],
NA [auth E],
OB [auth L],
OC [auth S],
PB [auth L],
PC [auth S],
SA [auth F],
SB [auth M],
TC [auth T],
VB [auth N],
X [auth A],
XA [auth G],
XB [auth O],
YB [auth O]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free:  0.234 (Depositor), 0.231 (DCC) 
  • R-Value Work:  0.222 (Depositor), 0.220 (DCC) 
  • R-Value Observed: 0.223 (Depositor) 
Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 207.35α = 90
b = 207.35β = 90
c = 545.471γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-01-19
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2023-12-20
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description