3HFT

Crystal structure of a putative polysaccharide deacetylase involved in o-antigen biosynthesis (wbms, bb0128) from bordetella bronchiseptica at 1.90 A resolution

• PDB DOI: https://doi.org/10.2210/pdb3HFT/pdb

• Classification: HYDROLASE
• Organism(s): Bordetella bronchiseptica
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-05-12 Released: 2009-06-23 
• Deposition Author(s): Joint Center for Structural Genomics, Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.184 
• R-Value Work: 0.162 
• R-Value Observed: 0.163 

Literature

Crystal structure of WbmS, polysaccharide deacetylase involved in O-antigen biosynthesis (NP_886680.1) from BORDETELLA BRONCHISEPTICA at 1.90 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content

• Total Structure Weight: 30.68 kDa 
• Atom Count: 2,215 
• Modelled Residue Count: 242 
• Deposited Residue Count: 257 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
WbmS, polysaccharide deacetylase involved in O-antigen biosynthesis	A	257	Bordetella bronchiseptica	Mutation(s): 0  Gene Names: BB0128, NP_886680.1, wbmS
UniProt
Find proteins for A0A0H3LGE5 (Bordetella bronchiseptica (strain ATCC BAA-588 / NCTC 13252 / RB50)) Explore A0A0H3LGE5  Go to UniProtKB:  A0A0H3LGE5

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MPD	I [auth A]	(4S)-2-METHYL-2,4-PENTANEDIOL C6 H14 O2 SVTBMSDMJJWYQN-YFKPBYRVSA-N
ZN	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO	D [auth A], E [auth A], F [auth A], G [auth A], H [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
UNL	C [auth A]	Unknown ligand 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: 1.90 Å
• R-Value Free: 0.184 
• R-Value Work: 0.162 
• R-Value Observed: 0.163 
• Space Group: P 4₁ 2₁ 2
• Diffraction Data: https://doi.org/10.18430/M33HFT

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.724	α = 90
b = 74.724	β = 90
c = 142.692	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
SHELXD	phasing
autoSHARP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-06-23 
Deposition Author(s): Joint Center for Structural Genomics, Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2009-06-23
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2017-11-01
  Changes: 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