6JDH

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)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.230
R-Value Work: 0.196
R-Value Observed: 0.198

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

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

Macromolecule Content

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

Macromolecules

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(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain F [auth B] MOL2 format, chain D [auth A] MOL2 format, chain F [auth B] mmCIF format, chain D [auth A] mmCIF format, chain F [auth B]	D [auth A], F [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain F [auth B] Interactions & Density Focus chain D [auth A] Focus chain F [auth B]
ZN (Subject of Investigation/LOI) Query on ZN Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain E [auth B] MOL2 format, chain C [auth A] MOL2 format, chain E [auth B] mmCIF format, chain C [auth A] mmCIF format, chain E [auth B]	C [auth A], E [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain E [auth B] Interactions & Density Focus chain C [auth A] Focus chain E [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.230
R-Value Work: 0.196
R-Value Observed: 0.198
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

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Entry History & Funding Information

Deposition Data

Released Date: 2020-02-05

Deposition Author(s):

Thanuja, G.

Ramaswamy, S.

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 (Full details and data files)

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

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6JDH

Crystal structure of N-acetyl mannosmaine kinase from Pasteurella multocida

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

Entity ID: 1

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Deposition Data

Revision History (Full details and data files)