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- PDB-1cqv: CRYSTAL STRUCTURE OF STAPHYLOCOCCAL ENTEROTOXIN C2 AT 100K CRYSTA... -

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Basic information

Entry
Database: PDB / ID: 1cqv
TitleCRYSTAL STRUCTURE OF STAPHYLOCOCCAL ENTEROTOXIN C2 AT 100K CRYSTALLIZED AT PH 5.0
ComponentsPROTEIN (STAPHYLOCOCCAL ENTEROTOXIN C2)
KeywordsTOXIN / ENTEROTOXIN / SUPERANTIGEN / ZINC BINDING / IMMUNE SYSTEM
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 REPLACEMEN / Resolution: 2.06 Å
AuthorsKumaran, D. / Swaminathan, S.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2001
Title: Structure of staphylococcal enterotoxin C2 at various pH levels.
Authors: Kumaran, D. / Eswaramoorthy, S. / Furey, W. / Sax, M. / Swaminathan, S.
#1: Journal: Nat.Struct.Biol. / Year: 1995
Title: Residues Defining V-Beta Specificity in Staphylococcal Enterotoxins
Authors: Swaminathan, S. / Furey, W. / Pletcher, J. / Sax, M.
#2: Journal: Acta Crystallogr.,Sect.D / Year: 1995
Title: Preliminary X-Ray Studies on Two New Crystal Forms of Staphylococcal Enterotoxin C2
Authors: Swaminathan, S. / Furey, W. / Pletcher, J. / Sax, M.
History
DepositionAug 11, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 22, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 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 / struct_site
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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 13, 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: PROTEIN (STAPHYLOCOCCAL ENTEROTOXIN C2)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,6882
Polymers27,6231
Non-polymers651
Water2,936163
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.683, 42.683, 289.149
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein PROTEIN (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.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 163 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsSIDE CHAIN ATOMS FOR RESIDUES 1,56,57,59,97,98,237 WERE NOT VISIBLE IN ELECTRON DENSITY MAP BEYOND CB ATOM

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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: 2.15 Å3/Da / Density % sol: 43.3 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 20% PEG 8000, 0.2M MAGNESIUM ACETATE, 0.1M CACODYLATE AT PH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal
*PLUS
Crystal grow
*PLUS
Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
15 mg/mlprotein1drop
220 %PEG80001reservoir
30.2 Mmagnesium acetate1reservoir
40.1 Msodium cacodylate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12B / Wavelength: 0.978
DetectorType: ADSC QUANTUM / Detector: CCD / Date: Jul 17, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 2.06→50 Å / Num. obs: 16187 / % possible obs: 89.4 % / Observed criterion σ(I): 0 / Redundancy: 5 % / Rmerge(I) obs: 0.03 / Net I/σ(I): 33.6
Reflection shellResolution: 2.05→2.12 Å / Rmerge(I) obs: 0.042 / % possible all: 45
Reflection
*PLUS
Highest resolution: 2.06 Å / Lowest resolution: 50 Å / % possible obs: 91.1 % / Observed criterion σ(I): 0 / Redundancy: 5 % / Num. measured all: 82018
Reflection shell
*PLUS
% possible obs: 48 % / Rmerge(I) obs: 0.05

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Processing

Software
NameClassification
ADSdata collection
SCALEPACKdata scaling
AMoREphasing
REFMACrefinement
ADSCdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMEN
Starting model: 1SE2

1se2


Resolution: 2.06→12.5 Å / SU B: 5.858 / SU ML: 0.153 / σ(F): 2 / ESU R: 0.234 / ESU R Free: 0.216
RfactorNum. reflectionSelection details
Rfree0.28 -RANDOM
Rwork0.208 --
obs-15179 -
Refinement stepCycle: LAST / Resolution: 2.06→12.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1865 0 1 163 2029
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.1870.02
X-RAY DIFFRACTIONp_angle_d0.2060.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0980.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it2.262
X-RAY DIFFRACTIONp_mcangle_it3.333
X-RAY DIFFRACTIONp_scbond_it2.732
X-RAY DIFFRACTIONp_scangle_it3.923
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor7.57
X-RAY DIFFRACTIONp_staggered_tor18.115
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor25.120
X-RAY DIFFRACTIONp_special_tor015
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.208 / Rfactor Rfree: 0.28
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_mcbond_it2.262
X-RAY DIFFRACTIONp_scbond_it2.732
X-RAY DIFFRACTIONp_mcangle_it3.333
X-RAY DIFFRACTIONp_scangle_it3.923

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