5LEO

Complex structure of lysostaphin SH3b domain with peptidoglycan fragment

PDB DOI: https://doi.org/10.2210/pdb5LEO/pdb

Classification: CELL ADHESION
Organism(s): Staphylococcaceae
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2016-06-30 Released: 2017-07-12
Deposition Author(s): Jagielska, E., Nowak, E., Bochtler, M., Sabala, I.
Funding Organization(s): The National Center for Research and Development

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free: 0.235
R-Value Work: 0.184
R-Value Observed: 0.187

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

Complex structure of lysostaphin SH3doamin with peptidoglycan fragment

Jagielska, E., Nowak, E., Bochtler, M., Sabala, I.

To be published.

Macromolecule Content

Total Structure Weight: 22.56 kDa
Atom Count: 1,838
Modelled Residue Count: 196
Deposited Residue Count: 198
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lysostaphin	A, B	94	Staphylococcaceae	Mutation(s): 0 Gene Names: lss EC: 3.4.24.75
UniProt
Find proteins for P10547 (Staphylococcus simulans) Explore P10547 Go to UniProtKB: P10547
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P10547
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
GLY-GLY-GLY-GLY-GLY	C [auth G], D [auth H]	5	Staphylococcaceae	Mutation(s): 0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MPD Query on MPD Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain L [auth B] MOL2 format, chain G [auth A] MOL2 format, chain L [auth B] mmCIF format, chain G [auth A] mmCIF format, chain L [auth B]	G [auth A], L [auth B]	(4S)-2-METHYL-2,4-PENTANEDIOL C₆ H₁₄ O₂ SVTBMSDMJJWYQN-YFKPBYRVSA-N		Interactions Focus chain G [auth A] Focus chain L [auth B] Interactions & Density Focus chain G [auth A] Focus chain L [auth B]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain H [auth B] SDF format, chain K [auth B] SDF format, chain E [auth A] SDF format, chain I [auth B] SDF format, chain J [auth B] MOL2 format, chain F [auth A] MOL2 format, chain H [auth B] MOL2 format, chain K [auth B] MOL2 format, chain E [auth A] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B] mmCIF format, chain F [auth A] mmCIF format, chain H [auth B] mmCIF format, chain K [auth B] mmCIF format, chain E [auth A] mmCIF format, chain I [auth B] mmCIF format, chain J [auth B]	E [auth A] F [auth A] H [auth B] I [auth B] J [auth B] E [auth A], F [auth A], H [auth B], I [auth B], J [auth B], K [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free: 0.235
R-Value Work: 0.184
R-Value Observed: 0.187
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.38	α = 90
b = 54.364	β = 90
c = 63.229	γ = 90

Software Package:

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

Structure Validation

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Entry History & Funding Information

Deposition Data

Released Date: 2017-07-12

Deposition Author(s):

Funding Organization	Location	Grant Number
The National Center for Research and Development	Poland	PBS1/A8/8/2012

Revision History (Full details and data files)

Version 1.0: 2017-07-12
Type: Initial release
Version 1.1: 2019-10-16
Changes: Data collection
Version 1.2: 2024-01-10
Changes: Data collection, Database references, Refinement description

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5LEO

Complex structure of lysostaphin SH3b domain with peptidoglycan fragment

Complex structure of lysostaphin SH3doamin with peptidoglycan fragment

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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