3DZM | pdb_00003dzm

Crystal structure of a major outer membrane protein from Thermus thermophilus HB27


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 
    0.234 (Depositor), 0.235 (DCC) 
  • R-Value Work: 
    0.196 (Depositor) 
  • R-Value Observed: 
    0.198 (Depositor) 

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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history

Literature

Crystal structure of a major outer membrane protein from Thermus thermophilus HB27

Brosig, A.Nesper, J.Boos, W.Welte, W.Diederichs, K.

(2009) J Mol Biology 385: 1445-1455

  • DOI: https://doi.org/10.1016/j.jmb.2008.12.003
  • Primary Citation Related Structures: 
    3DZM

  • PubMed Abstract: 

    The thermophilic eubacterium Thermus thermophilus belongs to one of the oldest branches of evolution and has a multilayered cell envelope that differs from that of modern Gram-negative bacteria. Its outer membrane contains integral outer membrane proteins (OMPs), of which only a few are characterized. TtoA, a new beta-barrel OMP, was identified by searching the genome sequence of strain HB27 for the presence of a C-terminal signature sequence. The structure of TtoA was determined to a resolution of 2.8 A, representing the first crystal structure of an OMP from a thermophilic bacterium. TtoA consists of an eight-stranded beta-barrel with a large extracellular part to which a divalent cation is bound. A five-stranded extracellular beta-sheet protrudes out of the membrane-embedded transmembrane barrel and is stabilized by a disulfide bridge. The edge of this beta-sheet forms crystal contacts that could mimic interactions with other proteins. In modern Gram-negative bacteria, the C-terminal signature sequence of OMPs is required for binding to an Omp85 family protein as a prerequisite for its assembly. We present hints that a similar assembly pathway exists in T. thermophilus by an in vitro binding assay, where unfolded TtoA binds to the Thermus Omp85 family protein TtOmp85, while a mutant without the signature sequence does not.


  • Organizational Affiliation
    • Department of Biology, University of Konstanz, Konstanz, Germany.

Macromolecule Content 

  • Total Structure Weight: 70.69 kDa 
  • Atom Count: 4,796 
  • Modeled Residue Count: 614 
  • Deposited Residue Count: 642 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Hypothetical conserved protein
A, B, C
214Thermus thermophilus HB27Mutation(s): 0 
Gene Names: TT_C0834
Membrane Entity: Yes 
UniProt
Find proteins for Q72JD8 (Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27))
Explore Q72JD8 
Go to UniProtKB:  Q72JD8
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ72JD8
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
C8E

Query on C8E



Download:Ideal Coordinates CCD File
E [auth A]
F [auth A]
H [auth B]
I [auth B]
K [auth C]
E [auth A],
F [auth A],
H [auth B],
I [auth B],
K [auth C],
L [auth C]
(HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE
C16 H34 O5
FEOZZFHAVXYAMB-UHFFFAOYSA-N
CA

Query on CA



Download:Ideal Coordinates CCD File
D [auth A],
G [auth B],
J [auth C]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free:  0.234 (Depositor), 0.235 (DCC) 
  • R-Value Work:  0.196 (Depositor) 
  • R-Value Observed: 0.198 (Depositor) 
Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 166.98α = 90
b = 166.98β = 90
c = 98.12γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
SHARPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-12-23
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Source and taxonomy, Version format compliance
  • Version 1.2: 2017-10-25
    Changes: Advisory, Refinement description
  • Version 1.3: 2024-11-13
    Changes: Advisory, Data collection, Database references, Derived calculations, Structure summary