4NP6

Crystal Structure of Adenylate Kinase from Vibrio cholerae O1 biovar eltor

• PDB DOI: https://doi.org/10.2210/pdb4NP6/pdb

• Classification: TRANSFERASE
• Organism(s): Vibrio cholerae O1 biovar El Tor str. N16961
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2013-11-20 Released: 2013-12-18 
• Deposition Author(s): Kim, Y., Zhou, M., Grimshaw, S., 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: 2.00 Å
• R-Value Free: 0.222 
• R-Value Work: 0.186 
• R-Value Observed: 0.188 

Literature

Crystal Structure of Adenylate Kinase from Vibrio cholerae O1 biovar eltor

Kim, Y., Zhou, M., Grimshaw, S., Anderson, W.F., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

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 and generated by PISA (software)

Biological Assembly 2  

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

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

Macromolecule Content

• Total Structure Weight: 95.25 kDa 
• Atom Count: 6,704 
• Modelled Residue Count: 858 
• Deposited Residue Count: 868 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Adenylate kinase	A, B, C, D	217	Vibrio cholerae O1 biovar El Tor str. N16961	Mutation(s): 0  Gene Names: adk, VC_0986 EC: 2.7.4.3
UniProt
Find proteins for Q9KTB7 (Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961)) Explore Q9KTB7  Go to UniProtKB:  Q9KTB7

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.222 
• R-Value Work: 0.186 
• R-Value Observed: 0.188 
• Space Group: P 4₃
• Diffraction Data: https://doi.org/10.18430/M34NP6

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 101.617	α = 90
b = 101.617	β = 90
c = 89.637	γ = 90

Software Package:

Software Name	Purpose
SBC-Collect	data collection
HKL-3000	data collection
HKL-3000	phasing
SHELXS	phasing
MLPHARE	phasing
DM	model building
ARP/wARP	model building
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
DM	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-12-18 
Deposition Author(s): Kim, Y., Zhou, M., Grimshaw, S., Anderson, W.F., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History  

• Version 1.0: 2013-12-18
  Type: Initial release
  
• Version 1.1: 2017-11-22
  Changes: Refinement description