1P9N

Crystal structure of Escherichia coli MobB.

• PDB DOI: https://doi.org/10.2210/pdb1P9N/pdb

• Classification: BIOSYNTHETIC PROTEIN
• Organism(s): Escherichia coli
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2003-05-12 Released: 2003-05-20 
• Deposition Author(s): Rangarajan, S.E., Tocilj, A., Li, Y., Iannuzzi, P., Matte, A., Cygler, M., Montreal-Kingston Bacterial Structural Genomics Initiative (BSGI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.308 
• R-Value Work: 0.275 
• R-Value Observed: 0.275 

Literature

Molecules of Escherichia coli MobB assemble into densely packed hollow cylinders in a crystal lattice with 75% solvent content.

Rangarajan, S.E., Tocilj, A., Li, Y., Iannuzzi, P., Matte, A., Cygler, M.

(2003) Acta Crystallogr D Biol Crystallogr 59: 2348-2352

• PubMed: 14646116 
• DOI: https://doi.org/10.1107/s090744490301967x
• Primary Citation of Related Structures:  
  1P9N


• PubMed Abstract: 
  

  The crystal structure of Escherichia coli MobB, an enzyme involved in the final step of molybdenum-cofactor biosynthesis, forms intertwined dimers. Each molecule consists of two segments and requires the second monomer for stable folding. Dimerization buries a quarter of the solvent-accessible area of the monomer. These dimers assemble into a hexagonal lattice with P6(4)22 symmetry and occupy only approximately 25% of the unit-cell volume. The symmetry-related dimers associate tightly into a helical structure with a diameter of 250 A and a pitch of 98 A. Two such helices are intertwined, shifted by 49 A along the sixfold axis. Within the crystal, these helices form thin-walled cylinders with an external diameter of 250 A and an internal diameter of 190 A. Their center is filled with solvent. These cylinders pack closely together, forming a hexagonal lattice with the highest possible packing density. This arrangement of dimers allows extensive intermolecular contacts with 75% solvent content in the crystal.

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Organizational Affiliation: 

Department of Biochemistry, McGill University, Canada.

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)

Macromolecule Content

• Total Structure Weight: 38.46 kDa 
• Atom Count: 2,605 
• Modelled Residue Count: 324 
• Deposited Residue Count: 340 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Molybdopterin-guanine dinucleotide biosynthesis protein B	A, B	170	Escherichia coli	Mutation(s): 5  Gene Names: MobB
UniProt
Find proteins for P32125 (Escherichia coli (strain K12)) Explore P32125  Go to UniProtKB:  P32125

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	C [auth A], D [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

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: 2.80 Å
• R-Value Free: 0.308 
• R-Value Work: 0.275 
• R-Value Observed: 0.275 
• Space Group: P 6₄ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 239.001	α = 90
b = 239.001	β = 90
c = 49.046	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2003-05-20 
Deposition Author(s): Rangarajan, S.E., Tocilj, A., Li, Y., Iannuzzi, P., Matte, A., Cygler, M., Montreal-Kingston Bacterial Structural Genomics Initiative (BSGI)

Revision History  

• Version 1.0: 2003-05-20
  Type: Initial release
  
• Version 1.1: 2008-04-29
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2018-01-31
  Changes: Experimental preparation