6JDH | pdb_00006jdh

Crystal structure of N-acetyl mannosmaine kinase from Pasteurella multocida

• PDB DOI: https://doi.org/10.2210/pdb6JDH/pdb

• Classification: SUGAR BINDING PROTEIN
• Organism(s): Pasteurella multocida
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2019-02-01 Released: 2020-02-05 
• Deposition Author(s): Thanuja, G., Ramaswamy, S.
• Funding Organization(s): Department of Biotechnology (India)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.230 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.196 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.198 (Depositor) 

Starting Model: experimental

Literature

Structure and Function of N‐Acetylmannosamine Kinases from Pathogenic Bacteria.

Thanuja, G., Ramaswamy, S.

(2020) ACS Omega 5: 30923-30926

• DOI: https://doi.org/10.1021/acsomega.0c03699

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)

Macromolecule Content 

• Total Structure Weight: 63.02 kDa 
• Atom Count: 4,730 
• Modeled Residue Count: 584 
• Deposited Residue Count: 594 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
N-acetylmannosamine kinase	A, B	297	Pasteurella multocida	Mutation(s): 0  Gene Names: nanK EC: 2.7.1.60

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	D [auth A], F [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN (Subject of Investigation/LOI)	C [auth A], E [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.230 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.196 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.198 (Depositor) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 126.336	α = 90
b = 126.336	β = 90
c = 82.42	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-02-05 
Deposition Author(s): Thanuja, G., Ramaswamy, S.

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Funding Organization	Location	Grant Number
Department of Biotechnology (India)	India	BT/IN/Sweden/06/SR/2017-18
Department of Biotechnology (India)	India	BT/PR12422/MED/31/287/ 2014

Revision History  

• Version 1.0: 2020-02-05
  Type: Initial release
  
• Version 1.1: 2020-12-16
  Changes: Database references
• Version 1.2: 2023-11-22
  Changes: Data collection, Database references, Refinement description