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- PDB-1uns: IDENTIFICATION OF A SECONDARY ZINC-BINDING SITE IN STAPHYLOCOCCAL... -

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Entry
Database: PDB / ID: 1uns
TitleIDENTIFICATION OF A SECONDARY ZINC-BINDING SITE IN STAPHYLOCOCCAL ENTEROTOXIN C2: IMPLICATIONS FOR SUPERANTIGEN RECOGNITION
ComponentsENTEROTOXIN TYPE C-2
KeywordsTOXIN / SUPERANTIGEN / ENTEROTOXIN / ZINC-BINDING SITE
Function / homology
Function and homology information


toxin activity / extracellular region / metal ion binding
Similarity search - Function
Staphylococcal enterotoxin/Streptococcal pyrogenic exotoxin signature 1. / Staphylococcal/streptococcal toxin, bacterial / Staphylococcal/Streptococcal toxin, OB-fold / Staphylococcal/Streptococcal toxin, OB-fold domain / Staphylococcal enterotoxin/Streptococcal pyrogenic exotoxin, conserved site / Staphyloccocal enterotoxin/Streptococcal pyrogenic exotoxin signature 2. / Ubiquitin-like (UB roll) - #120 / Superantigen, staphylococcal/streptococcal toxin, bacterial / Staphylococcal/Streptococcal toxin, beta-grasp domain / Staphylococcal/Streptococcal toxin, beta-grasp domain ...Staphylococcal enterotoxin/Streptococcal pyrogenic exotoxin signature 1. / Staphylococcal/streptococcal toxin, bacterial / Staphylococcal/Streptococcal toxin, OB-fold / Staphylococcal/Streptococcal toxin, OB-fold domain / Staphylococcal enterotoxin/Streptococcal pyrogenic exotoxin, conserved site / Staphyloccocal enterotoxin/Streptococcal pyrogenic exotoxin signature 2. / Ubiquitin-like (UB roll) - #120 / Superantigen, staphylococcal/streptococcal toxin, bacterial / Staphylococcal/Streptococcal toxin, beta-grasp domain / Staphylococcal/Streptococcal toxin, beta-grasp domain / Superantigen toxin, C-terminal / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #110 / Enterotoxin / Ubiquitin-like (UB roll) / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Roll / Beta Barrel / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Enterotoxin type C-2
Similarity search - Component
Biological speciesSTAPHYLOCOCCUS AUREUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsPapageorgiou, A.C. / Baker, M.D. / McLeod, J.D. / Goda, S. / Sansom, D.M. / Tranter, H.S. / Acharya, K.R.
Citation
Journal: J.Biol.Chem. / Year: 2004
Title: Identification of a Secondary Zinc-Binding Site in Staphylococcal Enterotoxin C2: Implications for Superantigen Recognition
Authors: Papageorgiou, A.C. / Baker, M.D. / Mcleod, J.D. / Goda, S. / Manzotti, C.N. / Sanson, D.M. / Tranter, H.S. / Acharya, K.R.
#1: Journal: Structure / Year: 1995
Title: Structure of the Superantigen Enterotoxin C2 from Staphylococcus Aureus Reveals a Zinc-Binding Site
Authors: Papageorgiou, A.C. / Acharya, K.R. / Shapiro, R. / Passalacqua, E.F. / Brehm, R.D. / Tranter, H.S.
#2: Journal: Bacterial Superantigens: Structure, Function and Therapeutic Potential
Year: 1995
Title: Molecular Topology is Important for the Function of Staphylococcal Superantigens
Authors: Tranter, H. / Brehm, R.D. / Acharya, K.R.
#3: Journal: Nature / Year: 1994
Title: Structural Basis of Superantigen Action Inferred from Crystal Structure of Toxic-Shock Syndrome Toxin-1
Authors: Acharya, K.R. / Passalacqua, E.F. / Jones, E.Y. / Harlos, K. / Stuart, D.I. / Brehm, R.D. / Tranter, H.S.
#4: Journal: J.Mol.Biol. / Year: 1993
Title: Crystallization and Preliminary X-Ray Analysis of a Microbial Superantigen Staphylococcal Enterotoxin C2
Authors: Passalacqua, E.F. / Brehm, R.D. / Acharya, K.R. / Tranter, H.S.
History
DepositionSep 15, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 13, 2003Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry
Revision 1.4Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ENTEROTOXIN TYPE C-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,7543
Polymers27,6231
Non-polymers1312
Water1,38777
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)42.500, 44.540, 131.650
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein ENTEROTOXIN TYPE C-2 / STAPHYLOCOCCAL ENTEROTOXIN C2 / SEC2


Mass: 27622.967 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) STAPHYLOCOCCUS AUREUS (bacteria) / References: UniProt: P34071
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 77 / Source method: isolated from a natural source / Formula: H2O
Compound detailsZINC ION A1237 IS TETRAHEDRALLY COORDINATED TO HIS 118, HIS 122 ASP 83 AND ASP 9 FROM A SYMMETRY ...ZINC ION A1237 IS TETRAHEDRALLY COORDINATED TO HIS 118, HIS 122 ASP 83 AND ASP 9 FROM A SYMMETRY RELATED MOLECULE. ZINC ION A1238 IS TETRAHEDRALLY COORDINATED TO HIS 47 AND GLU 7 FROM ONE MOLECULE AND GLU 119, AND GLU 80 FROM A SYMMETRY RELATED MOLECULE
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.26 Å3/Da / Density % sol: 45.46 %
Crystal growpH: 6.5 / Details: pH 6.50
Crystal grow
*PLUS
Temperature: 16 ℃ / pH: 6.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110 mg/mlprotein1drop
217-20 %PEG60001reservoir
30.02 %sodium azide1reservoir
40.1-10 mMzinc acetate1reservoir
50.1 Mcacodylate1reservoirpH6.5

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Data collection

DiffractionMean temperature: 289 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.5 / Wavelength: 0.88
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.88 Å / Relative weight: 1
ReflectionResolution: 2→40 Å / Num. obs: 16364 / % possible obs: 91.4 % / Observed criterion σ(I): -3 / Redundancy: 4.9 % / Rmerge(I) obs: 0.078
Reflection
*PLUS
Highest resolution: 2 Å / Lowest resolution: 40 Å / Num. measured all: 80816 / Rmerge(I) obs: 0.078
Reflection shell
*PLUS
Highest resolution: 2 Å / Lowest resolution: 2.06 Å / % possible obs: 72.1 % / Rmerge(I) obs: 0.297

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Processing

Software
NameVersionClassification
CNS3.1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1STE

1ste


Resolution: 2→8 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2254 -5 %RANDOM
Rwork0.1982 ---
obs0.1982 18932 97.9 %-
Displacement parametersBiso mean: 19.9 Å2
Refine analyzeLuzzati coordinate error obs: 0.25 Å
Refinement stepCycle: LAST / Resolution: 2→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1893 0 2 77 1972
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0059
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.18
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.5
X-RAY DIFFRACTIONc_mcangle_it2
X-RAY DIFFRACTIONc_scbond_it1.5
X-RAY DIFFRACTIONc_scangle_it2
Refinement
*PLUS
Lowest resolution: 40 Å / Num. reflection obs: 16330 / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: c_bond_d / Dev ideal: 0.006

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