3FEF | pdb_00003fef

Crystal structure of putative glucosidase lplD from bacillus subtilis

• PDB DOI: https://doi.org/10.2210/pdb3FEF/pdb

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


• Deposited: 2008-11-28 Released: 2008-12-30 
• Deposition Author(s): Ramagopal, U.A., Rajashankar, K.R., Toro, R., 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: 2.20 Å
• R-Value Free: 
  0.243 (Depositor), 0.236 (DCC) 
• R-Value Work: 
  0.187 (Depositor), 0.182 (DCC) 
• R-Value Observed: 
  0.190 (Depositor) 

Literature

Crystal structure of putative glucosidase lplD from bacillus subtilis.

Ramagopal, U.A., Rajashankar, K.R., Toro, R., Burley, S.K., Almo, S.C.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 generated by PISA (software)

Biological Assembly 2  

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

Biological assembly 2 generated by PISA (software)

Biological Assembly 3  

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

Biological assembly 3 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 202.87 kDa 
• Atom Count: 14,117 
• Modeled Residue Count: 1,736 
• Deposited Residue Count: 1,800 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative glucosidase lplD, ALPHA-GALACTURONIDASE	A, B, C, D	450	Bacillus subtilis	Mutation(s): 0  Gene Names: BSU07130, lplD EC: 3.2.1.67
UniProt
Find proteins for P39130 (Bacillus subtilis (strain 168)) Explore P39130  Go to UniProtKB:  P39130

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	E [auth A], F [auth A], H [auth B], I [auth B], K [auth C], M [auth D], N [auth D]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
MG	G [auth A], J [auth B], L [auth C], O [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B, C, D	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.243 (Depositor), 0.236 (DCC) 
• R-Value Work:  0.187 (Depositor), 0.182 (DCC) 
• R-Value Observed: 0.190 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 81.987	α = 69.8
b = 84.843	β = 68.1
c = 86.051	γ = 64.07

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-12-30 
Deposition Author(s): Ramagopal, U.A., Rajashankar, K.R., Toro, R., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History  

• Version 1.0: 2008-12-30
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2013-03-20
  Changes: Structure summary
• Version 1.3: 2017-11-01
  Changes: Refinement description
• Version 1.4: 2021-02-10
  Changes: Database references, Derived calculations, Structure summary
• Version 1.5: 2023-12-27
  Changes: Data collection, Database references, Refinement description
• Version 1.6: 2024-11-20
  Changes: Structure summary