4U12 | pdb_00004u12

Crystal structure of protein HP0242 from Helicobacter pylori at 1.94 A resolution: a knotted homodimer

• PDB DOI: https://doi.org/10.2210/pdb4U12/pdb
• Entry: 4U12 supersedes: 2OUF

• Classification: Structural Genomics, Unknown Function
• Organism(s): Helicobacter pylori 26695
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2014-07-14 Released: 2014-07-23 
• Deposition Author(s): Grabowski, M., Shabalin, I.G., Chruszcz, M., Skarina, T., Onopriyenko, O., Guthrie, J., Savchenko, A., Edwards, A., Joachimiak, A., Minor, W., Midwest Center for Structural Genomics (MCSG)
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.94 Å
• R-Value Free: 
  0.253 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.221 (Depositor), 0.230 (DCC) 
• R-Value Observed: 
  0.222 (Depositor) 

Literature

Crystal structure of protein HP0242 from Helicobacter pylori at 1.94 A resolution: a knotted homodimer

Grabowski, M., Shabalin, I.G., Chruszcz, M., Skarina, T., Onopriyenko, O., Guthrie, J., Savchenko, A., Edwards, A., Joachimiak, A., Minor, W.

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)

Macromolecule Content 

• Total Structure Weight: 11.2 kDa 
• Atom Count: 698 
• Modeled Residue Count: 80 
• Deposited Residue Count: 94 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uncharacterized protein HP0242	A	94	Helicobacter pylori 26695	Mutation(s): 0  Gene Names: C694_01225, HP_0242
UniProt
Find proteins for O25025 (Helicobacter pylori (strain ATCC 700392 / 26695)) Explore O25025  Go to UniProtKB:  O25025

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.94 Å
• R-Value Free:  0.253 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.221 (Depositor), 0.230 (DCC) 
• R-Value Observed: 0.222 (Depositor) 

Space Group: P 4₃ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.944	α = 90
b = 44.944	β = 90
c = 117.883	γ = 90

Software Package:

Software Name	Purpose
HKL-3000	data collection
HKL-3000	data reduction
HKL-3000	data scaling
SCALEPACK	data scaling
HKL-3000	phasing
SHELXDE	phasing
DM	phasing
RESOLVE	phasing
ARP	model building
Coot	model building
PDB_EXTRACT	data extraction
REFMAC	refinement

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2014-07-23 
Deposition Author(s): Grabowski, M., Shabalin, I.G., Chruszcz, M., Skarina, T., Onopriyenko, O., Guthrie, J., Savchenko, A., Edwards, A., Joachimiak, A., Minor, W., Midwest Center for Structural Genomics (MCSG)
• This entry supersedes: 2OUF

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R01-GM053163
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	U54-GM094585-04

Revision History  

• Version 1.0: 2014-07-23
  Type: Initial release
  
• Version 1.1: 2014-08-06
  Changes: Structure summary
• Version 1.2: 2017-09-20
  Changes: Author supporting evidence, Database references, Derived calculations, Other, Source and taxonomy
• Version 1.3: 2019-12-25
  Changes: Author supporting evidence
• Version 1.4: 2022-04-13
  Changes: Database references, Refinement description, Structure summary
• Version 1.5: 2023-12-27
  Changes: Data collection
• Version 1.6: 2024-11-13
  Changes: Structure summary