2O14

X-Ray Crystal Structure of Protein YXIM_BACsu from Bacillus subtilis. Northeast Structural Genomics Consortium Target SR595

• PDB DOI: https://doi.org/10.2210/pdb2O14/pdb

• Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
• Organism(s): Bacillus subtilis
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2006-11-28 Released: 2006-12-12 
• Deposition Author(s): Kuzin, A.P., Chen, Y., Seetharaman, J., Chen, C.X., Fang, Y., Cunningham, K., Ma, L.-C., Xiao, R., Liu, J., Baran, M.C., Acton, T.B., Rost, B., Montelione, G., Hunt, J.F., Tong, L., Northeast Structural Genomics Consortium (NESG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.205 
• R-Value Work: 0.189 
• R-Value Observed: 0.189 

Literature

X-Ray structure of the hypothetical protein YXIM_BACsu from Bacillus subtilis.

Kuzin, A.P., Chen, Y., Seetharaman, J., Chen, C., Fang, Y., Cunningham, K., Ma, L.-C., Xiao, R., Liu, J., Baran, M., Acton, T.B., Rost, B., Montelione, G.T., Hunt, J.F., Tong, L.

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: 41.79 kDa 
• Atom Count: 2,999 
• Modelled Residue Count: 354 
• Deposited Residue Count: 375 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hypothetical protein yxiM	A	375	Bacillus subtilis	Mutation(s): 9  EC: 3.1
UniProt
Find proteins for P42304 (Bacillus subtilis (strain 168)) Explore P42304  Go to UniProtKB:  P42304

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	C [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
MN	B [auth A]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N

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: 2.10 Å
• R-Value Free: 0.205 
• R-Value Work: 0.189 
• R-Value Observed: 0.189 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 85.425	α = 90
b = 59.774	β = 100.34
c = 92.388	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
ADSC	data collection
DENZO	data reduction
SCALEPACK	data scaling
SnB	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-12-12 
Deposition Author(s): Kuzin, A.P., Chen, Y., Seetharaman, J., Chen, C.X., Fang, Y., Cunningham, K., Ma, L.-C., Xiao, R., Liu, J., Baran, M.C., Acton, T.B., Rost, B., Montelione, G., Hunt, J.F., Tong, L., Northeast Structural Genomics Consortium (NESG)

Revision History  

• Version 1.0: 2006-12-12
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-10-18
  Changes: Refinement description
• Version 1.4: 2023-12-27
  Changes: Data collection, Database references, Derived calculations
• Version 1.5: 2024-10-16
  Changes: Structure summary