6JDA | pdb_00006jda

Crystal structure of N-acetyl mannosmaine kinase in complex with N-acetylmannosamine in Pasteurella multocida

• PDB DOI: https://doi.org/10.2210/pdb6JDA/pdb

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


• Deposited: 2019-01-31 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: 2.90 Å
• R-Value Free: 
  0.247 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.194 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.197 (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)

Biological Assembly Evidence: isothermal titration calorimetry

Macromolecule Content 

• Total Structure Weight: 31.07 kDa 
• Atom Count: 2,178 
• Modeled Residue Count: 291 
• Deposited Residue Count: 291 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
N-acetylmannosamine kinase	A	291	Pasteurella multocida	Mutation(s): 0  Gene Names: nanK EC: 2.7.1.60
UniProt
Find proteins for Q9CKB3 (Pasteurella multocida (strain Pm70)) Explore Q9CKB3  Go to UniProtKB:  Q9CKB3

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BM3 (Subject of Investigation/LOI)	B [auth A]	2-acetamido-2-deoxy-alpha-D-mannopyranose C8 H15 N O6 OVRNDRQMDRJTHS-UOLFYFMNSA-N
GOL	D [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN (Subject of Investigation/LOI)	C [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free:  0.247 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.194 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.197 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 103.816	α = 90
b = 173.732	β = 90
c = 48.06	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
PHASER	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: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary
• Version 1.2: 2020-12-16
  Changes: Database references, Structure summary
• Version 1.3: 2023-11-22
  Changes: Data collection, Database references, Refinement description