3I5V | pdb_00003i5v

Crystal structure of beta toxin 275-280 from Staphylococcus aureus

PDB DOI: https://doi.org/10.2210/pdb3I5V/pdb

Classification: TOXIN
Organism(s): Staphylococcus aureus subsp. aureus RN4220
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2009-07-06 Released: 2010-08-11
Deposition Author(s): Huseby, M., Shi, K., Kruse, A.C., Ohlendorf, D.H.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free:
0.267 (Depositor)
R-Value Work:
0.214 (Depositor), 0.233 (DCC)
R-Value Observed:
0.214 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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

Literature

Structure and biological functions of beta toxin from Staphylococcus aureus: Role of the hydrophobic beta hairpin in virulence

Huseby, M., Shi, K., Kruse, A.C., Digre, J., Mengistu, F., Bohach, G.A., Schlievert, P.S., Ohlendorf, D.H., Earhart, C.A.

To be published.

Macromolecule Content

Total Structure Weight: 142.87 kDa
Atom Count: 9,255
Modeled Residue Count: 1,139
Deposited Residue Count: 1,252
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-hemolysin	A, B, C, D	313	Staphylococcus aureus subsp. aureus RN4220	Mutation(s): 0 Gene Names: hlb EC: 3.1.4.3
UniProt
Find proteins for P09978 (Staphylococcus aureus) Explore P09978 Go to UniProtKB: P09978
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P09978
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
DGA Query on DGA Download:Ideal Coordinates CCD File SDF format, chain E [auth D] MOL2 format, chain E [auth D] mmCIF format, chain E [auth D]	E [auth D]	DIACYL GLYCEROL C₃₉ H₇₆ O₅ UHUSDOQQWJGJQS-QNGWXLTQSA-N		Interactions Focus chain E [auth D] Interactions & Density Focus chain E [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free: 0.267 (Depositor)
R-Value Work: 0.214 (Depositor), 0.233 (DCC)
R-Value Observed: 0.214 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.184	α = 93.06
b = 69.053	β = 94.6
c = 75.654	γ = 92.13

Software Package:

Software Name	Purpose
PDB_EXTRACT	data extraction
Blu-Ice	data collection
HKL-2000	data reduction
HKL-2000	data scaling
AMoRE	phasing
PHENIX	refinement

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2010-08-11

Deposition Author(s):

Ohlendorf, D.H.

Revision History (Full details and data files)

Version 1.0: 2010-08-11
Type: Initial release
Version 1.1: 2011-07-13
Changes: Source and taxonomy, Version format compliance
Version 1.2: 2024-04-03
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.3: 2024-10-30
Changes: 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.