2NP2 | pdb_00002np2

Hbb-DNA complex

• PDB DOI: https://doi.org/10.2210/pdb2NP2/pdb
• NAKB: 2NP2

• Classification: DNA BINDING PROTEIN/DNA
• Organism(s): Borreliella burgdorferi
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2006-10-26 Released: 2007-02-27 
• Deposition Author(s): Rice, P.A., Mouw, K.W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.02 Å
• R-Value Free: 
  0.276 (Depositor), 0.259 (DCC) 
• R-Value Work: 
  0.235 (Depositor), 0.218 (DCC) 
• R-Value Observed: 
  0.235 (Depositor) 

Starting Model: experimental

Literature

Shaping the Borrelia burgdorferi genome: crystal structure and binding properties of the DNA-bending protein Hbb.

Mouw, K.W., Rice, P.A.

(2007) Mol Microbiol 63: 1319-1330

• PubMed: 17244195 
• DOI: https://doi.org/10.1111/j.1365-2958.2007.05586.x
• Primary Citation Related Structures: 
  2NP2


• PubMed Abstract: 
  

  The genome of the Lyme disease-causing spirochete Borrelia burgdorferi encodes only a single polypeptide from the integration host factor (IHF)/HU or 'DNABII' family of nucleoid-associated proteins - Hbb. DNABII proteins induce large bends in DNA and serve as architectural factors in a variety of prokaryotic cellular processes. We have solved the crystal structure of an Hbb-DNA complex in which the DNA is bent by over 180 degrees . We find that like IHF, Hbb relies exclusively on indirect readout to recognize its cognate site. Additional binding studies show that the sequence preferences of Hbb are related to, yet distinct from those of IHF. Defining these binding characteristics may help to uncover additional roles for Hbb in Borrelia DNA metabolism as well as further our understanding of the mechanism of indirect readout.

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Organizational Affiliation: 
• Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, USA.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 47.51 kDa 
• Atom Count: 3,154 
• Modeled Residue Count: 276 
• Deposited Residue Count: 288 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Hbb	C [auth A], D [auth B]	108	Borreliella burgdorferi	Mutation(s): 0  Gene Names: hbb
UniProt
Find proteins for Q57267 (Borreliella burgdorferi (strain ATCC 35210 / DSM 4680 / CIP 102532 / B31)) Explore Q57267  Go to UniProtKB:  Q57267

Entity ID: 1
Molecule	Chains	Length	Organism	Image
36-MER	A [auth C], B [auth D]	36	N/A

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.02 Å
• R-Value Free:  0.276 (Depositor), 0.259 (DCC) 
• R-Value Work:  0.235 (Depositor), 0.218 (DCC) 
• R-Value Observed: 0.235 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.27	α = 90
b = 88.32	β = 90
c = 96.57	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-02-27 
Deposition Author(s): Rice, P.A., Mouw, K.W.

Revision History  

• Version 1.0: 2007-02-27
  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: 2023-08-30
  Changes: Data collection, Database references, Refinement description