4IIL

Crystal Structure of RfuA (TP0298) of T. pallidum Bound to Riboflavin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.3 Å
  • R-Value Free: 0.153 
  • R-Value Work: 0.121 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Evidence for an ABC-type riboflavin transporter system in pathogenic spirochetes.

Deka, R.K.Brautigam, C.A.Biddy, B.A.Liu, W.Z.Norgard, M.V.

(2013) MBio 4: e00615-e00612


Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Membrane lipoprotein TpN38(b)
A
346Treponema pallidum (strain Nichols)Gene Names: tpn38
Find proteins for Q56328 (Treponema pallidum (strain Nichols))
Go to UniProtKB:  Q56328
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
K
Query on K

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A
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

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A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
RBF
Query on RBF

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Download CCD File 
A
RIBOFLAVIN
RIBOFLAVINE; VITAMIN B2
C17 H20 N4 O6
AUNGANRZJHBGPY-SCRDCRAPSA-N
 Ligand Interaction
EDO
Query on EDO

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A
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.3 Å
  • R-Value Free: 0.153 
  • R-Value Work: 0.121 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 75.955α = 90.00
b = 107.790β = 90.00
c = 72.881γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
SBC-Collectdata collection
PHENIXrefinement
DENZOdata reduction
PDB_EXTRACTdata extraction
HKL-2000data reduction
PHENIXphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-02-27
    Type: Initial release
  • Version 1.1: 2013-04-17
    Type: Database references
  • Version 1.2: 2017-11-15
    Type: Refinement description