1TOA

PERIPLASMIC ZINC BINDING PROTEIN TROA FROM TREPONEMA PALLIDUM


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.176 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Treponema pallidum TroA is a periplasmic zinc-binding protein with a helical backbone.

Lee, Y.H.Deka, R.K.Norgard, M.V.Radolf, J.D.Hasemann, C.A.

(1999) Nat Struct Biol 6: 628-633

  • DOI: 10.1038/10677
  • Primary Citation of Related Structures:  
    1TOA

  • PubMed Abstract: 
  • The crystal structure of recombinant TroA, a zinc-binding protein component of an ATP-binding cassette transport system in Treponema pallidum, was determined at a resolution of 1.8 A. The organization of the protein is largely similar to other peripl ...

    The crystal structure of recombinant TroA, a zinc-binding protein component of an ATP-binding cassette transport system in Treponema pallidum, was determined at a resolution of 1.8 A. The organization of the protein is largely similar to other periplasmic ligand-binding proteins (PLBP), in that two independent globular domains interact with each other to create a zinc-binding cleft between them. The structure has one bound zinc pentavalently coordinated to residues from both domains. Unlike previous PLBP structures that have an interdomain hinge composed of beta-strands, the N- and C-domains of TroA are linked by a single long backbone helix. This unique backbone helical conformation was possibly adopted to limit the hinge motion associated with ligand exchange.


    Organizational Affiliation

    Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas 75235-8884, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PROTEIN (PERIPLASMIC BINDING PROTEIN TROA)AB313Treponema pallidumMutation(s): 0 
Find proteins for P96116 (Treponema pallidum (strain Nichols))
Explore P96116 
Go to UniProtKB:  P96116
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download CCD File 
A, B
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

Download CCD File 
A, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.176 
  • Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 126.2α = 90
b = 126.2β = 90
c = 74.48γ = 120
Software Package:
Software NamePurpose
MLPHAREphasing
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1999-07-05
    Type: Initial release
  • Version 1.1: 2007-10-16
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, Version format compliance