3HDX

Crystal structure of SusD superfamily protein (NP_809182.1) from BACTEROIDES THETAIOTAOMICRON VPI-5482 at 1.50 A resolution

• PDB DOI: https://doi.org/10.2210/pdb3HDX/pdb

• Classification: POLYSACCHARIDE BINDING PROTEIN
• Organism(s): Bacteroides thetaiotaomicron VPI-5482
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-05-07 Released: 2009-05-19 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.160 
• R-Value Work: 0.134 
• R-Value Observed: 0.136 

Literature

Crystal structure of SusD superfamily protein (NP_809182.1) from BACTEROIDES THETAIOTAOMICRON VPI-5482 at 1.50 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 55.86 kDa 
• Atom Count: 4,592 
• Modelled Residue Count: 456 
• Deposited Residue Count: 478 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SusD superfamily protein	A	478	Bacteroides thetaiotaomicron VPI-5482	Mutation(s): 0  Gene Names: BT_0269, NP_809182.1
UniProt
Find proteins for Q8AB42 (Bacteroides thetaiotaomicron (strain ATCC 29148 / DSM 2079 / JCM 5827 / CCUG 10774 / NCTC 10582 / VPI-5482 / E50)) Explore Q8AB42  Go to UniProtKB:  Q8AB42

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	B [auth A], C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.160 
• R-Value Work: 0.134 
• R-Value Observed: 0.136 
• Space Group: P 4₁ 2₁ 2
• Diffraction Data: https://doi.org/10.18430/M33HDX

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.221	α = 90
b = 56.221	β = 90
c = 301.899	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SHELX	phasing
MolProbity	model building
SCALA	data scaling
PDB_EXTRACT	data extraction
MOSFLM	data reduction
autoSHARP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-05-19 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2009-05-19
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-10-25
  Changes: Author supporting evidence, Refinement description
• Version 1.3: 2019-07-24
  Changes: Data collection, Derived calculations, Refinement description
• Version 1.4: 2023-02-01
  Changes: Database references, Derived calculations