3I76 | pdb_00003i76

The crystal structure of the orthorhombic form of the putative HAD-hydrolase YfnB from Bacillus subtilis bound to magnesium reveals interdomain movement

• PDB DOI: https://doi.org/10.2210/pdb3I76/pdb

• Classification: HYDROLASE
• Organism(s): Bacillus subtilis
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-07-08 Released: 2009-07-21 
• Deposition Author(s): Bonanno, J.B., Dickey, M., Bain, K.T., Tang, B.K., Romero, R., 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: 2.00 Å
• R-Value Free: 
  0.219 (Depositor), 0.213 (DCC) 
• R-Value Work: 
  0.175 (Depositor) 
• R-Value Observed: 
  0.177 (Depositor) 

Starting Model: experimental

Literature

The crystal structure of the orthorhombic form of the putative HAD-hydrolase YfnB from Bacillus subtilis bound to magnesium reveals interdomain movement

Bonanno, J.B., Dickey, M., Bain, K.T., Tang, B.K., Romero, R., 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)

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

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

Biological assembly 3 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 85.9 kDa 
• Atom Count: 6,007 
• Modeled Residue Count: 680 
• Deposited Residue Count: 732 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative HAD-hydrolase yfnB	A, B, C	244	Bacillus subtilis	Mutation(s): 0  Gene Names: BSU07330, yfnB EC: 3
UniProt
Find proteins for O06480 (Bacillus subtilis (strain 168)) Explore O06480  Go to UniProtKB:  O06480

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	F [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CL	E [auth A], G [auth A], I [auth B], L [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG	D [auth A], H [auth B], J [auth B], K [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.219 (Depositor), 0.213 (DCC) 
• R-Value Work:  0.175 (Depositor) 
• R-Value Observed: 0.177 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.685	α = 90
b = 67.964	β = 90
c = 271.404	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
MAR345	data collection
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-07-21 
Deposition Author(s): Bonanno, J.B., Dickey, M., Bain, K.T., Tang, B.K., Romero, R., Sauder, J.M., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History  

• Version 1.0: 2009-07-21
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.2: 2017-11-01
  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
• Version 1.5: 2023-09-06
  Changes: Data collection, Database references, Refinement description