[English] 日本語
Yorodumi
- PDB-1qoy: E.coli Hemolysin E (HlyE, ClyA, SheA) -

+
Open data


ID or keywords:

Loading...

-
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


hemolysis in another organism / toxin activity / periplasmic space / host cell plasma membrane / extracellular region / identical protein binding / membrane
Similarity search - Function
Hemolysin E / Haemolysin E (HlyE) / Hemolysin E; Chain: A; / Hemolysin E; Chain: A; - #10 / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

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

-
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

-
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 %

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more