4ZYS | pdb_00004zys

Crystal structure of an exotoxin 6 (SAV0422) from Staphylococcus aureus subsp. aureus Mu50 at 2.25 A resolution

PDB DOI: https://doi.org/10.2210/pdb4ZYS/pdb

Classification: SUGAR BINDING PROTEIN
Organism(s): Staphylococcus aureus subsp. aureus Mu50
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2015-05-22 Released: 2015-08-05
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.25 Å
R-Value Free:
0.240 (Depositor), 0.255 (DCC)
R-Value Work:
0.191 (Depositor), 0.203 (DCC)
R-Value Observed:
0.193 (Depositor)

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This is version 1.3 of the entry. See complete history.

Literature

Crystal structure of an exotoxin 6 (SAV0422) from Staphylococcus aureus subsp. aureus Mu50 at 2.25 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Macromolecule Content

Total Structure Weight: 45.96 kDa
Atom Count: 3,400
Modeled Residue Count: 386
Deposited Residue Count: 394
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
exotoxin 6	A, B	197	Staphylococcus aureus subsp. aureus Mu50	Mutation(s): 0 Gene Names: set6, NP_370946.1
UniProt
Find proteins for A0A0M3KL42 (Staphylococcus aureus (strain Mu50 / ATCC 700699)) Explore A0A0M3KL42 Go to UniProtKB: A0A0M3KL42
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A0M3KL42
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
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 B] SDF format, chain G [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth B] MOL2 format, chain G [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth B] mmCIF format, chain G [auth B]	C [auth A], D [auth A], E [auth A], F [auth B], G [auth B]	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 B] Focus chain G [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth B]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.25 Å
R-Value Free: 0.240 (Depositor), 0.255 (DCC)
R-Value Work: 0.191 (Depositor), 0.203 (DCC)
R-Value Observed: 0.193 (Depositor)

Diffraction Data:

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.12	α = 90
b = 64.02	β = 90
c = 98.98	γ = 90

Software Package:

Software Name	Purpose
PDB_EXTRACT	data extraction
SHELX	phasing
SHARP	phasing
XDS	data reduction
XSCALE	data scaling
SHELXD	phasing
BUSTER	refinement

Structure Validation

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Entry History

Deposition Data

Released Date: 2015-08-05

Deposition Author(s):

Joint Center for Structural Genomics (JCSG)

Revision History (Full details and data files)

Version 1.0: 2015-08-05
Type: Initial release
Version 1.1: 2018-01-24
Changes: Database references, Derived calculations
Version 1.2: 2023-02-01
Changes: Database references
Version 1.3: 2024-10-23
Changes: Data collection, Structure summary

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.