6O6D | pdb_00006o6d

N-terminal domain of translation initiation factor IF-3 from Helicobacter pylori

• PDB DOI: https://doi.org/10.2210/pdb6O6D/pdb

• Classification: LIGASE
• Organism(s): Helicobacter pylori J99
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2019-03-06 Released: 2019-03-13 
• Deposition Author(s): Osipiuk, J., Tesar, C., Endres, M., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.82 Å
• R-Value Free: 
  0.214 (Depositor), 0.211 (DCC) 
• R-Value Work: 
  0.175 (Depositor), 0.188 (DCC) 
• R-Value Observed: 
  0.177 (Depositor) 

Literature

N-terminal domain of translation initiation factor IF-3 from Helicobacter pylori

Osipiuk, J., Tesar, C., Endres, M., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 8.93 kDa 
• Atom Count: 558 
• Modeled Residue Count: 66 
• Deposited Residue Count: 80 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Translation initiation factor IF-3	A	80	Helicobacter pylori J99	Mutation(s): 0  Gene Names: infC, jhp_0114
UniProt
Find proteins for Q9ZMV2 (Helicobacter pylori (strain J99 / ATCC 700824)) Explore Q9ZMV2  Go to UniProtKB:  Q9ZMV2

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: 1.82 Å
• R-Value Free:  0.214 (Depositor), 0.211 (DCC) 
• R-Value Work:  0.175 (Depositor), 0.188 (DCC) 
• R-Value Observed: 0.177 (Depositor) 

Diffraction Data: https://doi.org/10.18430/m36o6d

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.468	α = 90
b = 56.468	β = 90
c = 55.142	γ = 90

Software Package:

Software Name	Purpose
HKL-3000	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-3000	data reduction
HKL-3000	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2019-03-13 
Deposition Author(s): Osipiuk, J., Tesar, C., Endres, M., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	HHSN272201200026C
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	HHSN272201700060C

Revision History  

• Version 1.0: 2019-03-13
  Type: Initial release
  
• Version 1.1: 2019-12-18
  Changes: Author supporting evidence
• Version 1.2: 2024-10-16
  Changes: Data collection, Database references, Structure summary