3F3B

Structure of the phage-like element PBSX protein xkdH from Bacillus Subtilus. Northeast Structural Genomics Consortium target SR352.

• PDB DOI: https://doi.org/10.2210/pdb3F3B/pdb

• Classification: structural genomics, unknown function
• Organism(s): Bacillus subtilis
• Mutation(s): No 


• Deposited: 2008-10-30 Released: 2008-11-25 
• Deposition Author(s): Kuzin, A.P., Neely, H., Seetharaman, J., Clayton, G., Ho, C.K., Janjua, H., Cunningham, K., Ma, L.-C., Xiao, R., Liu, J., Baran, M.C., Acton, T.B., Rost, B., 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: 2.50 Å
• R-Value Free: 0.263 
• R-Value Work: 0.230 
• R-Value Observed: 0.230 

Literature

Structure of the phage-like element PBSX protein xkdH from Bacillus Subtilus. Northeast Structural Genomics Consortium target SR352.

Kuzin, A.P., Neely, H., Seetharaman, J., Clayton, G., Ho, C.K., Cunningham, K., Ma, L.-C., Xiao, R., Liu, J., Baran, M.C., Acton, T.B., Rost, B., 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.

Macromolecule Content

• Total Structure Weight: 15.35 kDa 
• Atom Count: 1,031 
• Modelled Residue Count: 115 
• Deposited Residue Count: 126 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phage-like element PBSX protein xkdH	A	126	Bacillus subtilis	Mutation(s): 0  Gene Names: xkdH, BSU12620
UniProt
Find proteins for P54328 (Bacillus subtilis (strain 168)) Explore P54328  Go to UniProtKB:  P54328

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4	B [auth A], C [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.263 
• R-Value Work: 0.230 
• R-Value Observed: 0.230 
• Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.661	α = 90
b = 42.661	β = 90
c = 283.65	γ = 120

Software Package:

Software Name	Purpose
APEX	data collection
SnB	phasing
CNS	refinement
HKL-2000	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-11-25 
Deposition Author(s): Kuzin, A.P., Neely, H., Seetharaman, J., Clayton, G., Ho, C.K., Janjua, H., Cunningham, K., Ma, L.-C., Xiao, R., Liu, J., Baran, M.C., Acton, T.B., Rost, B., Montelione, G.T., Tong, L., Hunt, J.F., Northeast Structural Genomics Consortium (NESG)

Revision History  

• Version 1.0: 2008-11-25
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-10-25
  Changes: Refinement description
• Version 1.3: 2023-12-27
  Changes: Data collection, Database references, Derived calculations