6H4E | pdb_00006h4e

Proteus mirabilis N-acetylneuraminate lyase

• PDB DOI: https://doi.org/10.2210/pdb6H4E/pdb

• Classification: LYASE
• Organism(s): Proteus mirabilis HI4320
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2018-07-21 Released: 2019-06-26 
• Deposition Author(s): North, R.A., Garcia-Bonete, M.J., Goyal, P., Katona, G., Dobson, R.C.J., Friemann, R.
• Funding Organization(s): Royal Society of New Zealand, Swedish Research Council, European Molecular Biology Organization

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.56 Å
• R-Value Free: 
  0.181 (Depositor), 0.181 (DCC) 
• R-Value Work: 
  0.166 (Depositor), 0.167 (DCC) 
• R-Value Observed: 
  0.167 (Depositor) 

Starting Model: experimental

Literature

The structure of Proteus mirabilis N-acetylneuraminate lyase reveals an intermolecular disulphide bond

North, R.A., Garcia-Bonete, M.J., Goyal, P., Katona, G., Dobson, R.C.J., Friemann, R.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 63.51 kDa 
• Atom Count: 5,125 
• Modeled Residue Count: 590 
• Deposited Residue Count: 590 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative N-acetylneuraminate lyase	A, B	295	Proteus mirabilis HI4320	Mutation(s): 0  Gene Names: PMI2973
UniProt
Find proteins for B4EZY4 (Proteus mirabilis (strain HI4320)) Explore B4EZY4  Go to UniProtKB:  B4EZY4

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	C [auth A], D [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.56 Å
• R-Value Free:  0.181 (Depositor), 0.181 (DCC) 
• R-Value Work:  0.166 (Depositor), 0.167 (DCC) 
• R-Value Observed: 0.167 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 80.777	α = 90
b = 81.984	β = 90
c = 106.839	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2019-06-26 
Deposition Author(s): North, R.A., Garcia-Bonete, M.J., Goyal, P., Katona, G., Dobson, R.C.J., Friemann, R.

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Funding Organization	Location	Grant Number
Royal Society of New Zealand	New Zealand	UOC1506
Swedish Research Council	Sweden	2011-5790
Swedish Research Council	Sweden	2010-1759
European Molecular Biology Organization	New Zealand	584-2014

Revision History  

• Version 1.0: 2019-06-26
  Type: Initial release
  
• Version 1.1: 2024-01-17
  Changes: Data collection, Database references, Refinement description