2NWA | pdb_00002nwa

X-ray Crystal Structure of Protein ytmB from Bacillus subtilis. Northeast Structural Genomics Consortium Target SR466

• PDB DOI: https://doi.org/10.2210/pdb2NWA/pdb

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


• Deposited: 2006-11-14 Released: 2007-01-09 
• Deposition Author(s): Zhou, W., Forouhar, F., Seetharaman, J., Wang, D., Cunningham, K., Ma, L.-C., Fang, Y., Xiao, R., Baran, M.C., Acton, T.B., Montelione, G.T., Hunt, J.F., Tong, L., Northeast Structural Genomics Consortium (NESG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 
  0.285 (Depositor), 0.302 (DCC) 
• R-Value Work: 
  0.266 (Depositor), 0.284 (DCC) 
• R-Value Observed: 
  0.266 (Depositor) 

Literature

Crystal Structure of the Hypothetical protein YtmB from Bacillus subtilis subsp. (subtilis str. 168), Northeast Structural Genomics target SR466

Zhou, W., Forouhar, F., Seetharaman, J., Wang, D., Cunningham, K., Ma, L.-C., Fang, Y., Xiao, R., Baran, M.C., Acton, T.B., Montelione, G.T., Hunt, J.F., Tong, L.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

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

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

Biological Assembly 3  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 8-mer - A8 

Biological assembly 3 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 85.08 kDa 
• Atom Count: 5,356 
• Modeled Residue Count: 640 
• Deposited Residue Count: 704 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hypothetical protein ytmB	A, B, C, D, E, F, G, H	88	Bacillus subtilis	Mutation(s): 4  Gene Names: ytmB
UniProt
Find proteins for O34365 (Bacillus subtilis (strain 168)) Explore O34365  Go to UniProtKB:  O34365

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	I [auth A], J [auth B], K [auth C], L [auth D], M [auth E], N [auth F], O [auth G], P [auth H]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free:  0.285 (Depositor), 0.302 (DCC) 
• R-Value Work:  0.266 (Depositor), 0.284 (DCC) 
• R-Value Observed: 0.266 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.662	α = 90
b = 110.739	β = 111.06
c = 60.672	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
ADSC	data collection
HKL-2000	data reduction
HKL-2000	data scaling
SnB	phasing
SOLVE	phasing
RESOLVE	phasing
XTALVIEW	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-01-09 
Deposition Author(s): Zhou, W., Forouhar, F., Seetharaman, J., Wang, D., Cunningham, K., Ma, L.-C., Fang, Y., Xiao, R., Baran, M.C., Acton, T.B., Montelione, G.T., Hunt, J.F., Tong, L., Northeast Structural Genomics Consortium (NESG)

Revision History  

• Version 1.0: 2007-01-09
  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