4PI8 | pdb_00004pi8

Crystal structure of catalytic mutant E138A of S. Aureus Autolysin E in complex with disaccharide NAG-NAM

PDB DOI: https://doi.org/10.2210/pdb4PI8/pdb

Classification: HYDROLASE
Organism(s): Staphylococcus aureus subsp. aureus Mu50
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2014-05-08 Released: 2015-10-14
Deposition Author(s): Mihelic, M., Renko, M., Jakas, A., Turk, D.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.39 Å
R-Value Free:
0.175 (Depositor), 0.176 (DCC)
R-Value Work:
0.152 (Depositor), 0.152 (DCC)
R-Value Observed:
0.153 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 2.1 of the entry. See complete history.

Literature

The mechanism behind the selection of two different cleavage sites in NAG-NAM polymers

Mihelic, M., Vlahovicek-Kahlina, K., Renko, M., Mesnage, S., Dobersek, A., Taler-Vercic, A., Jakas, A., Turk, D.

(2017) IUCrJ 4: 185-198

DOI: https://doi.org/10.1107/S2052252517000367

Macromolecule Content

Total Structure Weight: 27.1 kDa
Atom Count: 2,146
Modeled Residue Count: 222
Deposited Residue Count: 228
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Autolysin E	A	228	Staphylococcus aureus subsp. aureus Mu50	Mutation(s): 1 Gene Names: SAV2307
UniProt
Find proteins for A0A0H3JT72 (Staphylococcus aureus (strain Mu50 / ATCC 700699)) Explore A0A0H3JT72 Go to UniProtKB: A0A0H3JT72
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A0H3JT72
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-N-acetyl-beta-muramic acid	B	2		N/A	Interactions Focus chain B Interactions & Density Focus chain B
Glycosylation Resources
GlyTouCan: G99515FY GlyCosmos: G99515FY

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain N [auth A] MOL2 format, chain N [auth A] mmCIF format, chain N [auth A]	N [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain N [auth A] Interactions & Density Focus chain N [auth A]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain O [auth A] SDF format, chain P [auth A] SDF format, chain Q [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain O [auth A] MOL2 format, chain P [auth A] MOL2 format, chain Q [auth A] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain M [auth A] mmCIF format, chain O [auth A] mmCIF format, chain P [auth A] mmCIF format, chain Q [auth A]	C [auth A] D [auth A] E [auth A] F [auth A] G [auth A] C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], O [auth A], P [auth A], Q [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.39 Å
R-Value Free: 0.175 (Depositor), 0.176 (DCC)
R-Value Work: 0.152 (Depositor), 0.152 (DCC)
R-Value Observed: 0.153 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.011	α = 90
b = 69.72	β = 90
c = 73.54	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
REFMAC	refinement
PDB_EXTRACT	data extraction
XSCALE	data scaling

Structure Validation

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Entry History

Deposition Data

Released Date: 2015-10-14

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2015-10-14
Type: Initial release
Version 1.1: 2017-03-08
Changes: Database references
Version 1.2: 2017-09-27
Changes: Author supporting evidence
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Structure summary
Version 2.1: 2023-12-27
Changes: Data collection, Database references, Derived calculations, Structure summary