4RFB | pdb_00004rfb

1.93 Angstrom Crystal Structure of Superantigen-like Protein from Staphylococcus aureus in Complex with Sialyl-Lewis X.

• PDB DOI: https://doi.org/10.2210/pdb4RFB/pdb

• Classification: TOXIN
• Organism(s): Staphylococcus aureus subsp. aureus NCTC 8325
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2014-09-25 Released: 2014-10-08 
• Deposition Author(s): Minasov, G., Nocadello, S., Shuvalova, L., Filippova, E.V., Halavaty, A., Dubrovska, I., Bagnoli, F., Falugi, F., Bottomley, M., Grandi, G., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.93 Å
• R-Value Free: 
  0.218 (Depositor), 0.222 (DCC) 
• R-Value Work: 
  0.169 (Depositor), 0.176 (DCC) 
• R-Value Observed: 
  0.171 (Depositor) 

Starting Model: experimental

Literature

1.93 Angstrom Crystal Structure of Superantigen-like Protein from Staphylococcus aureus in Complex with Sialyl-Lewis X.

Minasov, G., Nocadello, S., Shuvalova, L., Filippova, E.V., Halavaty, A., Dubrovska, I., Bagnoli, F., Falugi, F., Bottomley, M., Grandi, G., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 106.67 kDa 
• Atom Count: 7,321 
• Modeled Residue Count: 770 
• Deposited Residue Count: 872 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative uncharacterized protein	A, B, C, D	218	Staphylococcus aureus subsp. aureus NCTC 8325	Mutation(s): 0  Gene Names: SAOUHSC_00391
UniProt
Find proteins for Q2G1S5 (Staphylococcus aureus (strain NCTC 8325 / PS 47)) Explore Q2G1S5  Go to UniProtKB:  Q2G1S5

Oligosaccharides

Help  

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)]2-acetamido-2-deoxy-beta-D-glucopyranose	E, F, G, H	4		N/A
Glycosylation Resources
GlyTouCan: G00054MO GlyCosmos: G00054MO GlyGen: G00054MO

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PGE	N [auth B]	TRIETHYLENE GLYCOL C6 H14 O4 ZIBGPFATKBEMQZ-UHFFFAOYSA-N
PEG	K [auth A], P [auth C], Q [auth C]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
EDO	S [auth D]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL	I [auth A], J [auth A], L [auth B], M [auth B], O [auth C], R [auth D]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Biologically Interesting Molecules (External Reference) 

1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900121	E, F, G, H	Sialyl-Lewis X antigen, beta anomer	Oligosaccharide / Antigen

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.93 Å
• R-Value Free:  0.218 (Depositor), 0.222 (DCC) 
• R-Value Work:  0.169 (Depositor), 0.176 (DCC) 
• R-Value Observed: 0.171 (Depositor) 

Diffraction Data: https://doi.org/10.18430/m34rfb

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.64	α = 90
b = 108.199	β = 90
c = 167.655	γ = 90

Software Package:

Software Name	Purpose
Blu-Ice	data collection
PHASER	phasing
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-10-08 
Deposition Author(s): Minasov, G., Nocadello, S., Shuvalova, L., Filippova, E.V., Halavaty, A., Dubrovska, I., Bagnoli, F., Falugi, F., Bottomley, M., Grandi, G., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History  

• Version 1.0: 2014-10-08
  Type: Initial release
  
• Version 1.1: 2017-11-22
  Changes: Refinement description
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Database references, Derived calculations, Structure summary
• Version 2.1: 2023-09-20
  Changes: Data collection, Database references, Refinement description, Structure summary