Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

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

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

Biological Assembly 2  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 51.93 kDa 
• Atom Count: 3320 
• Modelled Residue Count: 403 
• Deposited Residue Count: 460 
• Unique protein chains: 1

3GMT

Crystal structure of adenylate kinase from burkholderia pseudomallei

• PDB DOI: 10.2210/pdb3GMT/pdb

• Classification: TRANSFERASE
• Organism(s): Burkholderia pseudomallei 1710b
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-03-15 Released: 2009-06-02 
• Deposition Author(s): Abendroth, J., Staker, B.L., Robinson, H., Buchko, G.W., Hewitt, S.N., Napuli, A.J., Van Voorhis, W., Stacy, R., Myler, P.J., Stewart, L., Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.295 
• R-Value Work: 0.235 
• R-Value Observed: 0.238 

Literature

Structural characterization of Burkholderia pseudomallei adenylate kinase (Adk): profound asymmetry in the crystal structure of the 'open' state.

Buchko, G.W., Robinson, H., Abendroth, J., Staker, B.L., Myler, P.J.

(2010) Biochem Biophys Res Commun 394: 1012-1017

• PubMed: 20331978 
• DOI: 10.1016/j.bbrc.2010.03.112
• Primary Citation of Related Structures:  
  3GMT


• PubMed Abstract: 
  

In all organisms adenylate kinases (Adks) play a vital role in cellular energy metabolism and nucleic acid synthesis. Due to differences in catalytic properties between the Adks found in prokaryotes and in the cytoplasm of eukaryotes, there is interest in targeting this enzyme for new drug therapies against infectious bacterial agents. Here we report the 2.1A resolution crystal structure for the 220-residue Adk from Burkholderia pseudomallei (BpAdk), the etiological agent responsible for the infectious disease melioidosis. The general structure of apo BpAdk is similar to other Adk structures, composed of a CORE subdomain with peripheral ATP-binding (ATP(bd)) and LID subdomains. The two molecules in the asymmetric unit have significantly different conformations, with a backbone RMSD of 1.46 A. These two BpAdk conformations may represent 'open' Adk sub-states along the preferential pathway to the 'closed' substrate-bound state.

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Related Citations: 

• Combining functional and structural genomics to sample the essential Burkholderia structome.
  Baugh, L., Gallagher, L.A., Patrapuvich, R., Clifton, M.C., Gardberg, A.S., Edwards, T.E., Armour, B., Begley, D.W., Dieterich, S.H., Dranow, D.M., Abendroth, J., Fairman, J.W., Fox, D., Staker, B.L., Phan, I., Gillespie, A., Choi, R., Nakazawa-Hewitt, S., Nguyen, M.T., Napuli, A., Barrett, L., Buchko, G.W., Stacy, R., Myler, P.J., Stewart, L.J., Manoil, C., Van Voorhis, W.C.
  (2013) PLoS One 8: e53851

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Organizational Affiliation: 

Biological Sciences Division and Seattle Structural Genomics Center for Infectious Disease, Pacific Northwest National Laboratory, Richland, WA 99352, USA. [e-mail]

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Adenylate kinase	A, B	230	Burkholderia pseudomallei 1710b	Mutation(s): 0  Gene Names: adk, BURPS1710b_1080 EC: 2.7.4.3
UniProt
Find proteins for Q3JVB1 (Burkholderia pseudomallei (strain 1710b)) Explore Q3JVB1  Go to UniProtKB:  Q3JVB1

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	C [auth A], D [auth A], E [auth B], F [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.295 
• R-Value Work: 0.235 
• R-Value Observed: 0.238 
• Space Group: P 1 2₁ 1
• Diffraction Data DOI: 10.18430/M33GMT Protein Diffraction

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.23	α = 90
b = 66	β = 113.69
c = 63.76	γ = 90

Software Package:

Software Name	Purpose
SHARP	phasing
PARROT	phasing
ARP/wARP	model building
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2009-03-15 
• Released Date: 2009-06-02 
Deposition Author(s): Abendroth, J., Staker, B.L., Robinson, H., Buchko, G.W., Hewitt, S.N., Napuli, A.J., Van Voorhis, W., Stacy, R., Myler, P.J., Stewart, L., Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History  

• Version 1.0: 2009-06-02
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2013-10-30
  Changes: Database references