3FX7 | pdb_00003fx7

Crystal structure of hypothetical protein of HP0062 from Helicobacter pylori

• PDB DOI: https://doi.org/10.2210/pdb3FX7/pdb

• Classification: UNKNOWN FUNCTION
• Organism(s): Helicobacter pylori
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-01-20 Released: 2009-09-01 
• Deposition Author(s): Kwon, A.R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 
  0.225 (Depositor), 0.229 (DCC) 
• R-Value Work: 
  0.186 (Depositor), 0.193 (DCC) 
• R-Value Observed: 
  0.188 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of Hypothetical Protein HP0062 (O24902_HELPY) from Helicobacter pylori at 1.65 A Resolution.

Jang, S.B., Kwon, A.R., Son, W.S., Park, S.J., Lee, B.J.

(2009) J Biochem 

• PubMed: 19564156 
• DOI: https://doi.org/10.1093/jb/mvp098
• Primary Citation Related Structures: 
  3FX7


• PubMed Abstract: 
  

  The HP0062 gene encodes a small acidic protein of 86 amino acids with a theoretical pI of 4.6. The crystal structure of hypothetical protein HP0062 from Helicobacter pylori has been determined at 1.65 A by molecular-replacement method. The crystallographic asymmetric unit contains dimer, in which HP0062 monomer folds into a helix-hairpin-helix structure. The two protomers are primarily held together by extensive hydrophobic interactions in an antiparallel arrangement, forming a four helix bundle. Aromatic residues located at a or g position in the heptad leucine zipper are not major contributor required for HP0062 dimerization but important for the thermostability of this protein.

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Organizational Affiliation: 
• Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, San 56-1, Shillim-Dong, Kwanak-Gu, Seoul 151-742, Korea.

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: 23.21 kDa 
• Atom Count: 1,654 
• Modeled Residue Count: 171 
• Deposited Residue Count: 188 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative uncharacterized protein	A, B	94	Helicobacter pylori	Mutation(s): 0  Gene Names: hp0062, HP_0062
UniProt
Find proteins for O24902 (Helicobacter pylori (strain ATCC 700392 / 26695)) Explore O24902  Go to UniProtKB:  O24902

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free:  0.225 (Depositor), 0.229 (DCC) 
• R-Value Work:  0.186 (Depositor), 0.193 (DCC) 
• R-Value Observed: 0.188 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 39.303	α = 90
b = 51.895	β = 90
c = 83.305	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
AMoRE	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-09-01 
Deposition Author(s): Kwon, A.R.

Revision History  

• Version 1.0: 2009-09-01
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-11-01
  Changes: Data collection, Database references, Refinement description