3IJ6 | pdb_00003ij6

CRYSTAL STRUCTURE OF AN UNCHARACTERIZED METAL-DEPENDENT HYDROLASE FROM Lactobacillus acidophilus

• PDB DOI: https://doi.org/10.2210/pdb3IJ6/pdb

• Classification: HYDROLASE
• Organism(s): Lactobacillus acidophilus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-08-03 Released: 2009-08-18 
• Deposition Author(s): Patskovsky, Y., Toro, R., Dickey, M., Chang, S., Sauder, J.M., Raushel, F.M., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.268 (Depositor), 0.270 (DCC) 
• R-Value Work: 
  0.221 (Depositor), 0.221 (DCC) 
• R-Value Observed: 
  0.222 (Depositor) 

Literature

CRYSTAL STRUCTURE OF AN UNCHARACTERIZED METAL-DEPENDENT HYDROLASE FROM Lactobacillus acidopphilus

Patskovsky, Y., Toro, R., Dickey, M., Chang, S., Sauder, J.M., Raushel, F.M., Burley, S.K., Almo, S.C.

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)

Biological Assembly 2  

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

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

Macromolecule Content 

• Total Structure Weight: 141.81 kDa 
• Atom Count: 10,133 
• Modeled Residue Count: 1,210 
• Deposited Residue Count: 1,248 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
UNCHARACTERIZED METAL-DEPENDENT HYDROLASE	A, B, C, D	312	Lactobacillus acidophilus	Mutation(s): 0  Gene Names: LBA1049
UniProt
Find proteins for Q5FK79 (Lactobacillus acidophilus (strain ATCC 700396 / NCK56 / N2 / NCFM)) Explore Q5FK79  Go to UniProtKB:  Q5FK79

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	E [auth A], G [auth B], I [auth C], K [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
NA	F [auth A], H [auth B], J [auth C], L [auth D]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.268 (Depositor), 0.270 (DCC) 
• R-Value Work:  0.221 (Depositor), 0.221 (DCC) 
• R-Value Observed: 0.222 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 170.717	α = 90
b = 96.433	β = 90.4
c = 96.033	γ = 90

Software Package:

Software Name	Purpose
SHELX	model building
RESOLVE	model building
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
SHELX	phasing
RESOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-08-18 
Deposition Author(s): Patskovsky, Y., Toro, R., Dickey, M., Chang, S., Sauder, J.M., Raushel, F.M., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History  

• Version 1.0: 2009-08-18
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2018-11-21
  Changes: Data collection, Structure summary
• Version 1.3: 2021-02-10
  Changes: Database references, Derived calculations, Structure summary
• Version 1.4: 2024-02-21
  Changes: Data collection, Database references