3LV4 | pdb_00003lv4

Crystal structure of the glycoside hydrolase, family 43 YxiA protein from Bacillus licheniformis. Northeast Structural Genomics Consortium Target BiR14.

• PDB DOI: https://doi.org/10.2210/pdb3LV4/pdb

• Classification: HYDROLASE
• Organism(s): Bacillus licheniformis DSM 13 = ATCC 14580
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2010-02-19 Released: 2010-03-09 
• Deposition Author(s): Vorobiev, S., Abashidze, M., Seetharaman, J., Belote, R.L., Ciccosanti, C., Sahdev, S., Xiao, R., Acton, T.B., Everett, J.K., Montelione, G.T., Tong, L., Hunt, J.F., Northeast Structural Genomics Consortium (NESG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.190 (Depositor), 0.180 (DCC) 
• R-Value Work: 
  0.146 (Depositor), 0.134 (DCC) 
• R-Value Observed: 
  0.149 (Depositor) 

Literature

Crystal structure of the glycoside hydrolase, family 43 YxiA protein from Bacillus licheniformis.

Vorobiev, S., Abashidze, M., Seetharaman, J., Belote, R.L., Ciccosanti, C., Sahdev, S., Xiao, R., Acton, T.B., Everett, J.K., Montelione, G.T., Tong, L., Hunt, J.F.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Biological Assembly Evidence: gel filtration

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: 104.06 kDa 
• Atom Count: 7,633 
• Modeled Residue Count: 880 
• Deposited Residue Count: 912 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycoside hydrolase YxiA	A, B	456	Bacillus licheniformis DSM 13 = ATCC 14580	Mutation(s): 0  Gene Names: BL00219, BLi04220, yxiA
UniProt
Find proteins for Q65D31 (Bacillus licheniformis (strain ATCC 14580 / DSM 13 / JCM 2505 / CCUG 7422 / NBRC 12200 / NCIMB 9375 / NCTC 10341 / NRRL NRS-1264 / Gibson 46)) Explore Q65D31  Go to UniProtKB:  Q65D31

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ACT	F [auth A], G [auth A], H [auth A], K [auth B], L [auth B]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
CA	C [auth A], D [auth A], E [auth A], I [auth B], J [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.190 (Depositor), 0.180 (DCC) 
• R-Value Work:  0.146 (Depositor), 0.134 (DCC) 
• R-Value Observed: 0.149 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 210.585	α = 90
b = 60.327	β = 97.47
c = 73.122	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
SHELXDE	phasing
PHENIX	model building
PHENIX	refinement
DENZO	data reduction
SCALEPACK	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-03-09 
Deposition Author(s): Vorobiev, S., Abashidze, M., Seetharaman, J., Belote, R.L., Ciccosanti, C., Sahdev, S., Xiao, R., Acton, T.B., Everett, J.K., Montelione, G.T., Tong, L., Hunt, J.F., Northeast Structural Genomics Consortium (NESG)

Revision History  

• Version 1.0: 2010-03-09
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-10-25
  Changes: Author supporting evidence, Refinement description
• Version 1.3: 2018-01-24
  Changes: Database references, Structure summary
• Version 1.4: 2024-10-30
  Changes: Data collection, Database references, Derived calculations, Structure summary