3L92 | pdb_00003l92

Phosphopantetheine adenylyltransferase from Yersinia pestis complexed with coenzyme A.

• PDB DOI: https://doi.org/10.2210/pdb3L92/pdb

• Classification: TRANSFERASE
• Organism(s): Yersinia pestis CO92
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2010-01-04 Released: 2010-01-19 
• Deposition Author(s): Osipiuk, J., Maltseva, N., Makowska-grzyska, M., Kwon, K., Anderson, W.F., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.89 Å
• R-Value Free: 
  0.192 (Depositor), 0.190 (DCC) 
• R-Value Work: 
  0.164 (Depositor), 0.160 (DCC) 
• R-Value Observed: 
  0.165 (Depositor) 

Starting Model: experimental

Literature

X-ray crystal structure of phosphopantetheine adenylyltransferase from Yersinia pestis.

Osipiuk, J., Maltseva, N., Makowska-grzyska, M., Kwon, K., Anderson, W.F., Joachimiak, A.

To be published.

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 2 generated by PISA (software)

Biological Assembly 3  

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

Biological assembly 3 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 18.72 kDa 
• Atom Count: 1,595 
• Modelled Residue Count: 159 
• Deposited Residue Count: 162 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphopantetheine adenylyltransferase	A	162	Yersinia pestis CO92	Mutation(s): 0  Gene Names: coaD, kdtB, y0088, YPO0053, YP_0054 EC: 2.7.7.3
UniProt
Find proteins for Q8ZJN9 (Yersinia pestis) Explore Q8ZJN9  Go to UniProtKB:  Q8ZJN9

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
COA	B [auth A]	COENZYME A C21 H36 N7 O16 P3 S RGJOEKWQDUBAIZ-IBOSZNHHSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.89 Å
• R-Value Free:  0.192 (Depositor), 0.190 (DCC) 
• R-Value Work:  0.164 (Depositor), 0.160 (DCC) 
• R-Value Observed: 0.165 (Depositor) 

Diffraction Data: https://doi.org/10.18430/m33l92

Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 114.82	α = 90
b = 114.82	β = 90
c = 119.074	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
SBC-Collect	data collection
HKL-3000	data reduction
MOLREP	phasing
HKL-3000	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-01-19 
Deposition Author(s): Osipiuk, J., Maltseva, N., Makowska-grzyska, M., Kwon, K., Anderson, W.F., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History  

• Version 1.0: 2010-01-19
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Refinement description, Version format compliance
• Version 1.2: 2014-10-01
  Changes: Structure summary
• Version 1.3: 2017-11-01
  Changes: Refinement description
• Version 1.4: 2023-09-06
  Changes: Data collection, Database references, Derived calculations, Refinement description