2GXF | pdb_00002gxf

X-Ray Crystal Structure of Protein YybH from Bacillus subtilis. Northeast Structural Genomics Consortium Target SR506.

• PDB DOI: https://doi.org/10.2210/pdb2GXF/pdb

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


• Deposited: 2006-05-08 Released: 2006-05-23 
• Deposition Author(s): Forouhar, F., Abashidze, M., Jayaraman, S., Cunningham, K., Fang, Y., Ma, L.-C., Xiao, R., Acton, T.B., Montelione, G.T., Hunt, J.F., Tong, L., Northeast Structural Genomics Consortium (NESG)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.10 Å
• R-Value Free: 
  0.286 (Depositor), 0.281 (DCC) 
• R-Value Work: 
  0.259 (Depositor), 0.264 (DCC) 
• R-Value Observed: 
  0.259 (Depositor) 

Literature

Crystal Structure of the Hypothetical Protein YybH from Bacillus subtilis, Northeast Structural Genomics Target SR506

Forouhar, F., Abashidze, M., Jayaraman, S., Cunningham, K., Fang, Y., Ma, L.-C., Xiao, R., Acton, T.B., Montelione, G.T., Hunt, J.F., Tong, L., Northeast Structural Genomics Consortium (NESG)

To be published.

Biological Assembly 1  

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

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

Biological Assembly 2  

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

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

Macromolecule Content

• Total Structure Weight: 66.42 kDa 
• Atom Count: 3,845 
• Modelled Residue Count: 476 
• Deposited Residue Count: 568 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hypothetical protein yybH	A, B, C, D	142	Bacillus subtilis	Mutation(s): 5  Gene Names: yybH
UniProt
Find proteins for P37496 (Bacillus subtilis (strain 168)) Explore P37496  Go to UniProtKB:  P37496

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MES	E [auth A], F [auth B], G [auth C], H [auth D]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C6 H13 N O4 S SXGZJKUKBWWHRA-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: 3.10 Å
• R-Value Free:  0.286 (Depositor), 0.281 (DCC) 
• R-Value Work:  0.259 (Depositor), 0.264 (DCC) 
• R-Value Observed: 0.259 (Depositor) 

Space Group: P 4₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 88.251	α = 90
b = 88.251	β = 90
c = 82.836	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
ADSC	data collection
DENZO	data reduction
SCALEPACK	data scaling
SHELX	phasing
SOLVE	phasing
RESOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-05-23 
Deposition Author(s): Forouhar, F., Abashidze, M., Jayaraman, S., Cunningham, K., Fang, Y., Ma, L.-C., Xiao, R., Acton, T.B., Montelione, G.T., Hunt, J.F., Tong, L., Northeast Structural Genomics Consortium (NESG)

Revision History  

• Version 1.0: 2006-05-23
  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: 2024-10-16
  Changes: Data collection, Database references, Derived calculations, Structure summary