3OTW | pdb_00003otw

Structural and Functional Studies of Helicobacter pylori Wild-Type and Mutated Proteins Phosphopantetheine adenylyltransferase

• PDB DOI: https://doi.org/10.2210/pdb3OTW/pdb

• Classification: TRANSFERASE
• Organism(s): Helicobacter pylori 26695
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2010-09-14 Released: 2011-09-14 
• Deposition Author(s): Yin, H.S., Cheng, C.S., Chen, C.G., Luo, Y.C., Chen, W.T., Cheng, S.Y.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.222 (Depositor), 0.248 (DCC) 
• R-Value Work: 
  0.186 (Depositor) 
• R-Value Observed: 
  0.188 (Depositor) 

Starting Model: experimental

Literature

Structural and Functional Studies of Helicobacter pylori Wild-Type and Mutated Proteins Phosphopantetheine adenylyltransferase

Yin, H.S., Cheng, C.S., Chen, C.G., Luo, Y.C., Chen, W.T., Cheng, S.Y.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D3  (Explore in 3D)
Global Stoichiometry: Homo 6-mer - A6 

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

Macromolecule Content 

• Total Structure Weight: 116.4 kDa 
• Atom Count: 8,355 
• Modeled Residue Count: 937 
• Deposited Residue Count: 978 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphopantetheine adenylyltransferase	A, B, C, D, E, F	163	Helicobacter pylori 26695	Mutation(s): 0  Gene Names: coaD, kdtB, HP_1475 EC: 2.7.7.3
UniProt
Find proteins for O26010 (Helicobacter pylori (strain ATCC 700392 / 26695)) Explore O26010  Go to UniProtKB:  O26010

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
COA	H [auth A], K [auth B], M [auth C], O [auth D], R [auth E], S [auth F]	COENZYME A C21 H36 N7 O16 P3 S RGJOEKWQDUBAIZ-IBOSZNHHSA-N
SO4	G [auth A], I [auth B], J [auth B], L [auth C], N [auth D], P [auth E], Q [auth E]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.222 (Depositor), 0.248 (DCC) 
• R-Value Work:  0.186 (Depositor) 
• R-Value Observed: 0.188 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.419	α = 90
b = 119.846	β = 90
c = 124.573	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-09-14 
Deposition Author(s): Yin, H.S., Cheng, C.S., Chen, C.G., Luo, Y.C., Chen, W.T., Cheng, S.Y.

Revision History  

• Version 1.0: 2011-09-14
  Type: Initial release
  
• Version 1.1: 2023-11-01
  Changes: Data collection, Database references, Derived calculations, Refinement description