3CGH

Crystal structure of a susd homolog (bt_3984) from bacteroides thetaiotaomicron vpi-5482 at 1.70 A resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.166 
  • R-Value Work: 0.140 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure of BT_3984, a member of the SusD/RagB family of nutrient-binding molecules.

Bakolitsa, C.Xu, Q.Rife, C.L.Abdubek, P.Astakhova, T.Axelrod, H.L.Carlton, D.Chen, C.Chiu, H.J.Clayton, T.Das, D.Deller, M.C.Duan, L.Ellrott, K.Farr, C.L.Feuerhelm, J.Grant, J.C.Grzechnik, A.Han, G.W.Jaroszewski, L.Jin, K.K.Klock, H.E.Knuth, M.W.Kozbial, P.Krishna, S.S.Kumar, A.Lam, W.W.Marciano, D.McMullan, D.Miller, M.D.Morse, A.T.Nigoghossian, E.Nopakun, A.Okach, L.Puckett, C.Reyes, R.Tien, H.J.Trame, C.B.van den Bedem, H.Weekes, D.Hodgson, K.O.Wooley, J.Elsliger, M.A.Deacon, A.M.Godzik, A.Lesley, S.A.Wilson, I.A.

(2010) Acta Crystallogr.,Sect.F 66: 1274-1280

  • DOI: 10.1107/S1744309110032999

  • PubMed Abstract: 
  • The crystal structure of the Bacteroides thetaiotaomicron protein BT_3984 was determined to a resolution of 1.7 Å and was the first structure to be determined from the extensive SusD family of polysaccharide-binding proteins. SusD is an essential com ...

    The crystal structure of the Bacteroides thetaiotaomicron protein BT_3984 was determined to a resolution of 1.7 Å and was the first structure to be determined from the extensive SusD family of polysaccharide-binding proteins. SusD is an essential component of the sus operon that defines the paradigm for glycan utilization in dominant members of the human gut microbiota. Structural analysis of BT_3984 revealed an N-terminal region containing several tetratricopeptide repeats (TPRs), while the signature C-terminal region is less structured and contains extensive loop regions. Sequence and structure analysis of BT_3984 suggests the presence of binding interfaces for other proteins from the polysaccharide-utilization complex.


    Organizational Affiliation

    Program on Bioinformatics and Systems Biology, Sanford-Burnham Medical Research Institute, La Jolla, CA, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
SusD homolog
A
516Bacteroides thetaiotaomicron (strain ATCC 29148 / DSM 2079 / NCTC 10582 / E50 / VPI-5482)Mutation(s): 0 
Find proteins for Q8A0N7 (Bacteroides thetaiotaomicron (strain ATCC 29148 / DSM 2079 / NCTC 10582 / E50 / VPI-5482))
Go to UniProtKB:  Q8A0N7
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
ACT
Query on ACT

Download SDF File 
Download CCD File 
A
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

Unit Cell:
Length (Å)Angle (°)
a = 49.780α = 90.00
b = 125.270β = 90.00
c = 174.650γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
autoSHARPphasing
MAR345data collection
REFMACrefinement
PHENIXrefinement
PDB_EXTRACTdata extraction
SHELXphasing
XSCALEdata scaling
SHELXDphasing
MolProbitymodel building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-03-18
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Version format compliance
  • Version 1.2: 2017-10-25
    Type: Refinement description