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- PDB-1qoy: E.coli Hemolysin E (HlyE, ClyA, SheA) -

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Basic information

Entry
Database: PDB / ID: 1qoy
TitleE.coli Hemolysin E (HlyE, ClyA, SheA)
ComponentsHEMOLYSIN E
KeywordsTOXIN / MEMBRANE PORE FORMER / CYTOLYSIN / HEMOLYSIN / PORES
Function / homology
Function and homology information


modulation of apoptotic process in another organism / hemolysis in another organism / toxin activity / periplasmic space / host cell plasma membrane / extracellular region / identical protein binding / membrane
Similarity search - Function
Hemolysin E; Chain: A; / Hemolysin E; Chain: A; - #10 / Hemolysin E / Haemolysin E (HlyE) / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Hemolysin E, chromosomal
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2 Å
AuthorsWallace, A.J. / Stillman, T.J. / Atkins, A. / Jamieson, S.J. / Bullough, P.A. / Green, J. / Artymiuk, P.J.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2000
Title: E. Coli Hemolysin E (Hlye, Clya, Shea): X-Ray Crystal Structure of the Toxin and Observation of Membrane Pores by Electron Microscopy
Authors: Wallace, A.J. / Stillman, T.J. / Atkins, A. / Jamieson, S.J. / Bullough, P.A. / Green, J. / Artymiuk, P.J.
History
DepositionNov 25, 1999Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 23, 2000Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 24, 2018Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain
Revision 1.4May 8, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HEMOLYSIN E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,1022
Polymers35,0061
Non-polymers961
Water6,107339
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)84.470, 84.470, 142.690
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 HEMOLYSIN E / CYTOLYSIN A / SILENT HEMOLYSIN A / HLYE / CLYA / SHEA


Mass: 35005.707 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: K12 / Cellular location: CYTOPLASM / Gene: HLYE / Plasmid: PGEX-KG-HLYE / Cellular location (production host): CYTOPLASM / Gene (production host): HLYE / Production host: ESCHERICHIA COLI K-12 (bacteria) / References: UniProt: P77335
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 339 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHE INTIAL 15 RESIDUES, GSPGISGGGGGILDS, ARE THE GST LINKER. THE T2A MUTATION WAS A RESULT OF A ...THE INTIAL 15 RESIDUES, GSPGISGGGGGILDS, ARE THE GST LINKER. THE T2A MUTATION WAS A RESULT OF A ENGINEERED NCO1 RESTRICTION SITE THE A187V MUATION IS THE RESULT OF A SINGLE BASE MUTATION IN THE CODON FOR ALANINE 187
Sequence detailsTHE SWISSPROT ENTRY HLYE_ECOLI REPORTS AN INCORRECT N-TERMINAL REGION OF THE PROTEIN THAT CONTAINS ...THE SWISSPROT ENTRY HLYE_ECOLI REPORTS AN INCORRECT N-TERMINAL REGION OF THE PROTEIN THAT CONTAINS A FRAMESHIFT ERROR THAT TRUNCATES THE PROTEIN. THE CORRECT SEQUENCE IS GIVEN IN EMBL ECU57430 (SV U57430.1). THE FIRST 10 RESIDUES FROM EACH DATA BASE ARE, ECU57430 : MIMTEIVADK HLYE_ECOLI : MTEIVADKTV

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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: 3.74 Å3/Da / Density % sol: 67.1 %
Crystal growpH: 6 / Details: pH 6.00
Crystal grow
*PLUS
pH: 6.8 / Method: vapor diffusion, hanging drop
Details: drop consists of equal volume of protein and reservoir solutions
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlprotein1drop
225 mMTris-HCl1drop
3100 mM1dropNaCl
42.5 mM1dropCaCl2
51.1 Mammonium sulfate1reservoir
610 mM1reservoirCoCl2
7100 mMMES1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX7.2 / Wavelength: 1.488
DetectorType: ADSC QUANTUM 4 CCD / Detector: CCD / Date: May 29, 1998 / Details: PLATINUM COATED MIRRORS
RadiationMonochromator: GE(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.488 Å / Relative weight: 1
ReflectionResolution: 2→17.8 Å / Num. obs: 31955 / % possible obs: 89.3 % / Redundancy: 2.5 % / Biso Wilson estimate: 22.5 Å2 / Rmerge(I) obs: 0.036 / Net I/σ(I): 12
Reflection shellResolution: 2→2.05 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.056 / Mean I/σ(I) obs: 7.6 / % possible all: 72
Reflection
*PLUS
Num. measured all: 78696
Reflection shell
*PLUS
% possible obs: 72 %

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Processing

Software
NameClassification
REFMACrefinement
MOSFLMdata reduction
Agrovatadata scaling
ROTAVATAdata scaling
CCP4phasing
RefinementMethod to determine structure: MIR / Resolution: 2→17.8 Å / SU ML: 0.095 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.158 / ESU R Free: 0.161
RfactorNum. reflection% reflectionSelection details
Rfree0.252 1586 5 %RANDOM
Rwork0.198 ---
obs-31510 89.3 %-
Displacement parametersBiso mean: 29.7 Å2
Refinement stepCycle: LAST / Resolution: 2→17.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2371 0 5 339 2715
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0110.02
X-RAY DIFFRACTIONp_angle_d0.030.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0340.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr0.1080.15
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: REFMAC / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_dihedral_angle_d
X-RAY DIFFRACTIONp_dihedral_angle_deg15.1

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