4JB3 | pdb_00004jb3

Crystal structure of BT_0970, a had family phosphatase from bacteroides thetaiotaomicron VPI-5482, TARGET EFI-501083, with bound sodium and glycerol, closed lid, ordered loop

• PDB DOI: https://doi.org/10.2210/pdb4JB3/pdb

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


• Deposited: 2013-02-19 Released: 2013-03-13 
• Deposition Author(s): Vetting, M.W., Toro, R., Bhosle, R., Kumar, P.R., Ghosh, A., Al Obaidi, N.F., Stead, M., Washington, E., Scott Glenn, A., Chowdhury, S., Evans, B., Hammonds, J., Hillerich, B., Love, J., Seidel, R.D., Imker, H.J., Dunaway-Mariano, D., Allen, K.N., Gerlt, J.A., Almo, S.C., Enzyme Function Initiative (EFI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 
  0.172 (Depositor), 0.174 (DCC) 
• R-Value Work: 
  0.146 (Depositor), 0.148 (DCC) 
• R-Value Observed: 
  0.147 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of bt_0970, a had family phosphatase from bacteroides thetaiotaomicron VPI-5482, TARGET EFI-501083, with bound sodium and glycerol, closed lid, ordered loop

Vetting, M.W., Toro, R., Bhosle, R., Kumar, P.R., Ghosh, A., Al Obaidi, N.F., Stead, M., Washington, E., Scott Glenn, A., Chowdhury, S., Evans, B., Hammonds, J., Hillerich, B., Love, J., Seidel, R.D., Imker, H.J., Dunaway-Mariano, D., Allen, K.N., 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: 26.24 kDa 
• Atom Count: 2,005 
• Modeled Residue Count: 218 
• Deposited Residue Count: 228 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Haloacid dehalogenase-like hydrolase	A	228	Bacteroides thetaiotaomicron VPI-5482	Mutation(s): 0  Gene Names: BT_0970 EC: 3.1.3 (UniProt), 3.1.3.104 (UniProt)
UniProt
Find proteins for Q8A947 (Bacteroides thetaiotaomicron (strain ATCC 29148 / DSM 2079 / JCM 5827 / CCUG 10774 / NCTC 10582 / VPI-5482 / E50)) Explore Q8A947  Go to UniProtKB:  Q8A947

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	C [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
NA	B [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free:  0.172 (Depositor), 0.174 (DCC) 
• R-Value Work:  0.146 (Depositor), 0.148 (DCC) 
• R-Value Observed: 0.147 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.58	α = 90
b = 91.19	β = 104.22
c = 46.27	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
MOSFLM	data reduction
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-03-13 
Deposition Author(s): Vetting, M.W., Toro, R., Bhosle, R., Kumar, P.R., Ghosh, A., Al Obaidi, N.F., Stead, M., Washington, E., Scott Glenn, A., Chowdhury, S., Evans, B., Hammonds, J., Hillerich, B., Love, J., Seidel, R.D., Imker, H.J., Dunaway-Mariano, D., Allen, K.N., Gerlt, J.A., Almo, S.C., Enzyme Function Initiative (EFI)

Revision History  

• Version 1.0: 2013-03-13
  Type: Initial release
  
• Version 1.1: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description