3NIW

Crystal structure of a haloacid dehalogenase-like hydrolase from Bacteroides thetaiotaomicron

• PDB DOI: https://doi.org/10.2210/pdb3NIW/pdb

• Classification: Structural Genomics, Unknown function
• Organism(s): Bacteroides thetaiotaomicron
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2010-06-16 Released: 2010-06-30 
• Deposition Author(s): Bonanno, J.B., Ramagopal, U., Toro, R., Rutter, M., Bain, K.T., Wu, B., Sauder, J.M., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.206 
• R-Value Work: 0.177 
• R-Value Observed: 0.178 

Literature

Crystal structure of a haloacid dehalogenase-like hydrolase from Bacteroides thetaiotaomicron

Bonanno, J.B., Ramagopal, U., Toro, R., Rutter, M., Bain, K.T., Wu, B., Sauder, J.M., Burley, S.K., Almo, S.C.

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: 31.74 kDa 
• Atom Count: 2,201 
• 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	Mutation(s): 0  Gene Names: BT_3352
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
GOL	C [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
MG	B [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-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: 0.206 
• R-Value Work: 0.177 
• R-Value Observed: 0.178 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.773	α = 90
b = 72.716	β = 90
c = 82.4	γ = 90

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
HKL-2000	data reduction
HKL-2000	data scaling
SHELXCD	phasing
SHELXE	model building
Coot	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-06-30 
Deposition Author(s): Bonanno, J.B., Ramagopal, U., Toro, R., Rutter, M., Bain, K.T., Wu, B., Sauder, J.M., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History  

• Version 1.0: 2010-06-30
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-11-08
  Changes: Refinement description
• Version 1.3: 2018-11-21
  Changes: Data collection, Structure summary
• Version 1.4: 2021-02-10
  Changes: Database references, Derived calculations, Structure summary