4DW8

Crystal structure of a haloacid dehalogenase-like hydrolase (Target EFI-900331) from Bacteroides thetaiotaomicron with bound Na crystal form I

• PDB DOI: https://doi.org/10.2210/pdb4DW8/pdb

• Classification: HYDROLASE
• Organism(s): Bacteroides thetaiotaomicron VPI-5482
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2012-02-24 Released: 2012-03-28 
• Deposition Author(s): Vetting, M.W., Wasserman, S.R., Morisco, L.L., Sojitra, S., Allen, K.N., Dunaway-Mariano, D., Imker, H.J., Gerlt, J.A., Almo, S.C., Enzyme Function Initiative (EFI)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.211 
• R-Value Work: 0.181 
• R-Value Observed: 0.182 

Starting Model: experimental

Literature

Crystal structure of a haloacid dehalogenase-like hydrolase (Target EFI-900331) from Bacteroides thetaiotaomicron with bound Na crystal form I

Vetting, M.W., Wasserman, S.R., Morisco, L.L., Sojitra, S., Allen, K.N., Dunaway-Mariano, D., Imker, H.J., Gerlt, J.A., Almo, S.C., Enzyme Function Initiative (EFI)

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)

Macromolecule Content

• Total Structure Weight: 31.22 kDa 
• Atom Count: 2,384 
• Modelled Residue Count: 266 
• Deposited Residue Count: 279 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Haloacid dehalogenase-like hydrolase	A	279	Bacteroides thetaiotaomicron VPI-5482	Mutation(s): 0  Gene Names: BT_3352 EC: 3.8.1
UniProt
Find proteins for Q8A2F3 (Bacteroides thetaiotaomicron (strain ATCC 29148 / DSM 2079 / JCM 5827 / CCUG 10774 / NCTC 10582 / VPI-5482 / E50)) Explore Q8A2F3  Go to UniProtKB:  Q8A2F3

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NA	E [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N
UNL	B [auth A], C [auth A], D [auth A]	Unknown ligand FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.211 
• R-Value Work: 0.181 
• R-Value Observed: 0.182 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.669	α = 90
b = 73.133	β = 90
c = 82.572	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
MAR345	data collection
HKL-3000	data reduction
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-03-28 
Deposition Author(s): Vetting, M.W., Wasserman, S.R., Morisco, L.L., Sojitra, S., Allen, K.N., Dunaway-Mariano, D., Imker, H.J., Gerlt, J.A., Almo, S.C., Enzyme Function Initiative (EFI)

Revision History  

• Version 1.0: 2012-03-28
  Type: Initial release
  
• Version 1.1: 2017-11-15
  Changes: Refinement description
• Version 1.2: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description