4DB3 | pdb_00004db3

1.95 Angstrom Resolution Crystal Structure of N-acetyl-D-glucosamine kinase from Vibrio vulnificus.

• PDB DOI: https://doi.org/10.2210/pdb4DB3/pdb

• Classification: TRANSFERASE
• Organism(s): Vibrio vulnificus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2012-01-13 Released: 2012-01-25 
• Deposition Author(s): Minasov, G., Wawrzak, Z., Onopriyenko, O., Skarina, T., Papazisi, L., Savchenko, A., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 
  0.198 (Depositor), 0.201 (DCC) 
• R-Value Work: 
  0.168 (Depositor), 0.174 (DCC) 
• R-Value Observed: 
  0.170 (Depositor) 

Starting Model: experimental

Literature

1.95 Angstrom Resolution Crystal Structure of N-acetyl-D-glucosamine kinase from Vibrio vulnificus.

Minasov, G., Wawrzak, Z., Onopriyenko, O., Skarina, T., Papazisi, L., Savchenko, A., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 35.68 kDa 
• Atom Count: 2,608 
• Modeled Residue Count: 311 
• Deposited Residue Count: 327 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
N-acetyl-D-glucosamine kinase	A	327	Vibrio vulnificus	Mutation(s): 0  Gene Names: nagK, VV1_2570 EC: 2.7.1.59
UniProt
Find proteins for Q8D9M7 (Vibrio vulnificus (strain CMCP6)) Explore Q8D9M7  Go to UniProtKB:  Q8D9M7

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	E [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	F [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
CL	C [auth A], D [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free:  0.198 (Depositor), 0.201 (DCC) 
• R-Value Work:  0.168 (Depositor), 0.174 (DCC) 
• R-Value Observed: 0.170 (Depositor) 

Diffraction Data: https://doi.org/10.18430/m34db3

Space Group: P 6₄

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 80.4	α = 90
b = 80.4	β = 90
c = 110.418	γ = 120

Software Package:

Software Name	Purpose
Blu-Ice	data collection
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-01-25 
Deposition Author(s): Minasov, G., Wawrzak, Z., Onopriyenko, O., Skarina, T., Papazisi, L., Savchenko, A., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History  

• Version 1.0: 2012-01-25
  Type: Initial release
  
• Version 1.1: 2017-11-15
  Changes: Refinement description
• Version 1.2: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description