1LNZ

Structure of the Obg GTP-binding protein

• PDB DOI: https://doi.org/10.2210/pdb1LNZ/pdb

• Classification: CELL CYCLE
• Organism(s): Bacillus subtilis
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2002-05-04 Released: 2002-09-16 
• Deposition Author(s): Buglino, J., Shen, V., Hakimian, P., Lima, C.D., Burley, S.K., New York SGX Research Center for Structural Genomics (NYSGXRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.293 
• R-Value Work: 0.203 
• R-Value Observed: 0.203 

Literature

Structural and biochemical analysis of the Obg GTP binding protein

Buglino, J., Shen, V., Hakimian, P., Lima, C.D.

(2002) Structure 10: 1581-1592

• PubMed: 12429099 
• DOI: https://doi.org/10.1016/s0969-2126(02)00882-1
• Primary Citation of Related Structures:  
  1LNZ


• PubMed Abstract: 
  

  The Obg nucleotide binding protein family has been implicated in stress response, chromosome partitioning, replication initiation, mycelium development, and sporulation. Obg proteins are among a large group of GTP binding proteins conserved from bacteria to man. Members of the family contain two equally and highly conserved domains, a C-terminal GTP binding domain and an N-terminal glycine-rich domain. Structural analysis of Bacillus subtilis Obg revealed respective domain architectures and how they are coupled through the putative switch elements of the C-terminal GTPase domain in apo and nucleotide-bound configurations. Biochemical analysis of bacterial and human Obg proteins combined with the structural observation of the ppGpp nucleotide within the Obg active sight suggest a potential role for ppGpp modulation of Obg function in B. subtilis.

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Organizational Affiliation: 

Biochemistry Department, Structural Biology Program, Weill Medical College of Cornell University, New York, NY 10021, USA.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 76.99 kDa 
• Atom Count: 5,608 
• Modelled Residue Count: 662 
• Deposited Residue Count: 684 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SPO0B-associated GTP-binding protein	A, B	342	Bacillus subtilis	Mutation(s): 0  EC: 3.6.5
UniProt
Find proteins for P20964 (Bacillus subtilis (strain 168)) Explore P20964  Go to UniProtKB:  P20964

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
G4P	J [auth B]	GUANOSINE-5',3'-TETRAPHOSPHATE C10 H17 N5 O17 P4 BUFLLCUFNHESEH-UUOKFMHZSA-N
MG	C [auth A], D [auth A], E [auth B], F [auth B], G [auth B], H [auth B], I [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-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: 2.60 Å
• R-Value Free: 0.293 
• R-Value Work: 0.203 
• R-Value Observed: 0.203 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.58	α = 90
b = 105.006	β = 90
c = 124.098	γ = 90

Software Package:

Software Name	Purpose
SHARP	phasing
CNS	refinement
HKL-2000	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2002-09-16 
Deposition Author(s): Buglino, J., Shen, V., Hakimian, P., Lima, C.D., Burley, S.K., New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History  

• Version 1.0: 2002-09-16
  Type: Initial release
  
• Version 1.1: 2008-04-28
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2021-02-03
  Changes: Database references, Derived calculations, Structure summary