3HBZ

Crystal structure of a putative glycoside hydrolase (bt_2081) from bacteroides thetaiotaomicron vpi-5482 at 2.05 A resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.191 
  • R-Value Work: 0.159 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure of Bacteroides thetaiotaomicron BT2081 at 2.05 A resolution: the first structural representative of a new protein family that may play a role in carbohydrate metabolism.

Yeh, A.P.Abdubek, P.Astakhova, T.Axelrod, H.L.Bakolitsa, C.Cai, X.Carlton, D.Chen, C.Chiu, H.J.Chiu, M.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.Wooten, T.Xu, Q.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: 1287-1296

  • DOI: 10.1107/S1744309110028228

  • PubMed Abstract: 
  • BT2081 from Bacteroides thetaiotaomicron (GenBank accession code NP_810994.1) is a member of a novel protein family consisting of over 160 members, most of which are found in the different classes of Bacteroidetes. Genome-context analysis lends suppo ...

    BT2081 from Bacteroides thetaiotaomicron (GenBank accession code NP_810994.1) is a member of a novel protein family consisting of over 160 members, most of which are found in the different classes of Bacteroidetes. Genome-context analysis lends support to the involvement of this family in carbohydrate metabolism, which plays a key role in B. thetaiotaomicron as a predominant bacterial symbiont in the human distal gut microbiome. The crystal structure of BT2081 at 2.05 Å resolution represents the first structure from this new protein family. BT2081 consists of an N-terminal domain, which adopts a β-sandwich immunoglobulin-like fold, and a larger C-terminal domain with a β-sandwich jelly-roll fold. Structural analyses reveal that both domains are similar to those found in various carbohydrate-active enzymes. The C-terminal β-jelly-roll domain contains a potential carbohydrate-binding site that is highly conserved among BT2081 homologs and is situated in the same location as the carbohydrate-binding sites that are found in structurally similar glycoside hydrolases (GHs). However, in BT2081 this site is partially occluded by surrounding loops, which results in a deep solvent-accessible pocket rather than a shallower solvent-exposed cleft.


    Organizational Affiliation

    Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park,CA, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
putative glycoside hydrolase
A
342Bacteroides thetaiotaomicron (strain ATCC 29148 / DSM 2079 / NCTC 10582 / E50 / VPI-5482)Mutation(s): 0 
Find proteins for Q8A605 (Bacteroides thetaiotaomicron (strain ATCC 29148 / DSM 2079 / NCTC 10582 / E50 / VPI-5482))
Go to UniProtKB:  Q8A605
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

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Download CCD File 
A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
ACT
Query on ACT

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A
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
CA
Query on CA

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Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
P6G
Query on P6G

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A
HEXAETHYLENE GLYCOL
POLYETHYLENE GLYCOL PEG400
C12 H26 O7
IIRDTKBZINWQAW-UHFFFAOYSA-N
 Ligand Interaction
PEG
Query on PEG

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Download CCD File 
A
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
CAC
Query on CAC

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A
CACODYLATE ION
dimethylarsinate
C2 H6 As O2
OGGXGZAMXPVRFZ-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 = 94.551α = 90.00
b = 94.551β = 90.00
c = 107.812γ = 120.00
Software Package:
Software NamePurpose
PHENIXrefinement
MolProbitymodel building
SHELXphasing
MOSFLMdata reduction
SHELXDphasing
REFMACrefinement
SCALAdata scaling
PDB_EXTRACTdata extraction
autoSHARPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-05-26
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Version format compliance
  • Version 1.2: 2017-10-25
    Type: Author supporting evidence, Refinement description