4I1V | pdb_00004i1v

Crystal structure of a dephospho-CoA kinase from Burkholderia vietnamiensis bound to ADP

• PDB DOI: https://doi.org/10.2210/pdb4I1V/pdb

• Classification: TRANSFERASE
• Organism(s): Burkholderia vietnamiensis G4
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2012-11-21 Released: 2013-01-09 
• Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 
  0.252 (Depositor), 0.249 (DCC) 
• R-Value Work: 
  0.213 (Depositor), 0.214 (DCC) 
• R-Value Observed: 
  0.215 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of a dephospho-CoA kinase from Burkholderia vietnamiensis bound to ADP

Edwards, T.E., Clifton, M.C., Sankaran, B., Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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.

Macromolecule Content 

• Total Structure Weight: 46.75 kDa 
• Atom Count: 3,070 
• Modeled Residue Count: 409 
• Deposited Residue Count: 420 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dephospho-CoA kinase	A, B	210	Burkholderia vietnamiensis G4	Mutation(s): 0  Gene Names: Bcep1808_0550, coaE EC: 2.7.1.24
UniProt
Find proteins for A4JBA9 (Burkholderia vietnamiensis (strain G4 / LMG 22486)) Explore A4JBA9  Go to UniProtKB:  A4JBA9

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ADP	C [auth A], D [auth B]	ADENOSINE-5'-DIPHOSPHATE C10 H15 N5 O10 P2 XTWYTFMLZFPYCI-KQYNXXCUSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free:  0.252 (Depositor), 0.249 (DCC) 
• R-Value Work:  0.213 (Depositor), 0.214 (DCC) 
• R-Value Observed: 0.215 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M34I1V

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 115.86	α = 90
b = 115.86	β = 90
c = 91.64	γ = 120

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-01-09 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History  

• Version 1.0: 2013-01-09
  Type: Initial release
  
• Version 1.1: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description