[English] 日本語
Yorodumi
- PDB-1qnu: Shiga-Like Toxin I B Subunit Complexed with the Bridged-Starfish ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1qnu
TitleShiga-Like Toxin I B Subunit Complexed with the Bridged-Starfish Inhibitor
ComponentsShiga toxin 1 variant B subunit
KeywordsTOXIN / SUBNANOMOLAR INHIBITOR / MULTIVALENT PROTEIN-CARBOHYDRATE RECOGNITION / OB-FOLD
Function / homology
Function and homology information


symbiont-mediated modulation of host virulence / hemolysis by symbiont of host erythrocytes / extracellular region
Similarity search - Function
OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #70 / Shiga-like toxin, beta subunit / Shiga-like toxin beta subunit / Enterotoxin / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
METHYL-CARBAMIC ACID ETHYL ESTER / ETHYL-CARBAMIC ACID METHYL ESTER / Shiga toxin 1 variant B subunit / Shiga toxin I subunit B
Similarity search - Component
Biological speciesEscherichia coli O157:H7 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.23 Å
AuthorsPannu, N.S. / Hayakawa, K. / Read, R.J.
Citation
Journal: Nature / Year: 2000
Title: Shiga-like toxins are neutralized by tailored multivalent carbohydrate ligands.
Authors: Kitov, P.I. / Sadowska, J.M. / Mulvey, G. / Armstrong, G.D. / Ling, H. / Pannu, N.S. / Read, R.J. / Bundle, D.R.
#1: Journal: Biochemistry / Year: 1998
Title: Structure of the Shiga-Like Toxin I B-Pentamer Complexed with an Analogue of its Receptor Bg3
Authors: Ling, H. / Boodhoo, A. / Hazes, B. / Cummings, M.D. / Armstrong, G.D. / Brunton, J.L. / Read, R.J.
History
DepositionOct 21, 1999Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 11, 2000Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 30, 2018Group: Data collection / Structure summary / Category: struct / Item: _struct.title
Revision 1.4Jun 13, 2018Group: Data collection / Database references ...Data collection / Database references / Source and taxonomy / Structure summary
Category: citation / entity ...citation / entity / entity_src_gen / struct_ref / struct_ref_seq
Item: _citation.page_last / _citation.title ..._citation.page_last / _citation.title / _entity.pdbx_description / _entity_src_gen.pdbx_beg_seq_num / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name / _entity_src_gen.pdbx_seq_type / _struct_ref.db_code / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.pdbx_db_accession
Revision 1.5May 8, 2019Group: Data collection / Derived calculations / Experimental preparation
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / struct_conn
Item: _exptl_crystal_grow.method / _struct_conn.pdbx_leaving_atom_flag
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_validate_chiral / pdbx_validate_close_contact / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.occupancy / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_database_status.status_code_sf / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_comp_id / _pdbx_validate_chiral.auth_seq_id / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_seq_id_1 / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _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_symmetry / _struct_conn.ptnr2_auth_asym_id / _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_symmetry
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Revision 2.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Shiga toxin 1 variant B subunit
B: Shiga toxin 1 variant B subunit
C: Shiga toxin 1 variant B subunit
D: Shiga toxin 1 variant B subunit
E: Shiga toxin 1 variant B subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,04720
Polymers38,4935
Non-polymers3,55315
Water1,44180
1
A: Shiga toxin 1 variant B subunit
B: Shiga toxin 1 variant B subunit
C: Shiga toxin 1 variant B subunit
D: Shiga toxin 1 variant B subunit
E: Shiga toxin 1 variant B subunit
hetero molecules

A: Shiga toxin 1 variant B subunit
B: Shiga toxin 1 variant B subunit
C: Shiga toxin 1 variant B subunit
D: Shiga toxin 1 variant B subunit
E: Shiga toxin 1 variant B subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,09340
Polymers76,98610
Non-polymers7,10730
Water18010
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area17830 Å2
ΔGint-84.1 kcal/mol
Surface area33650 Å2
MethodPQS
Unit cell
Length a, b, c (Å)104.470, 71.610, 56.360
Angle α, β, γ (deg.)90.00, 109.02, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.382759, 0.89895, -0.213035), (-0.898579, 0.308693, -0.311871), (0.214594, 0.310801, 0.925933)-0.018, 0.085, -0.013
2given(-0.616651, 0.553131, -0.560167), (-0.551662, -0.811247, -0.193769), (-0.561614, 0.189535, 0.805398)0.06, 0.101, 0.063
3given(-0.612174, -0.555757, -0.562474), (0.557655, -0.807756, 0.19118), (-0.560592, -0.196631, 0.804408)0.078, 0.064, 0.114
4given(0.387512, -0.896514, -0.214701), (0.896586, 0.312356, 0.313953), (-0.2144, -0.314159, 0.924844)0.009, -0.068, 0.081
DetailsBIOLOGICAL_UNIT: PENTAMER

-
Components

#1: Protein
Shiga toxin 1 variant B subunit / VEROTOXIN I B SUBUNIT


Mass: 7698.634 Da / Num. of mol.: 5 / Fragment: RECEPTOR-BINDING DOMAIN
Source method: isolated from a genetically manipulated source
Details: COMPLEXED WITH BRIDGE-STARFISH MOLECULE, A SUBNANOMOLAR TAILORED MULTIVALENT INHIBITOR
Source: (gene. exp.) Escherichia coli O157:H7 (bacteria) / Gene: stx1 / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q7WZI6, UniProt: V5URS0*PLUS
#2: Polysaccharide
beta-D-galactopyranose-(1-4)-beta-D-galactopyranose-(1-4)-alpha-D-glucopyranose


Type: oligosaccharide / Mass: 504.438 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGalpb1-4DGalpb1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1a_1-5][a2112h-1b_1-5]/1-2-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(4+1)][b-D-Galp]{[(4+1)][a-D-Galp]{}}}LINUCSPDB-CARE
#3: Chemical
ChemComp-EMB / METHYL-CARBAMIC ACID ETHYL ESTER


Mass: 103.120 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C4H9NO2
#4: Chemical
ChemComp-MEC / ETHYL-CARBAMIC ACID METHYL ESTER


Mass: 103.120 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C4H9NO2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 80 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.39 Å3/Da / Density % sol: 49 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 7
Details: COMPLEX PREPARED BY ADDING 15 MICROLITRES OF BRIDGE-STARFIS (0.35MM) SLOWLY TO 15 MICROLITRES OF SLT-I B-SUBUNIT (10 MG WHILE AGITATING. HANGING DROPS WERE PREPARED BY MIXING THI SOLUTION ...Details: COMPLEX PREPARED BY ADDING 15 MICROLITRES OF BRIDGE-STARFIS (0.35MM) SLOWLY TO 15 MICROLITRES OF SLT-I B-SUBUNIT (10 MG WHILE AGITATING. HANGING DROPS WERE PREPARED BY MIXING THI SOLUTION WITH AN EQUAL VOLUME OF RESERVOIR SOLUTION (28% SA NH4SO4, 2% 2-METHYL-2,4-PENTANEDIOL, 0.1M NACL, 0.1 M HEPES, pH 7.00
Crystal grow
*PLUS
pH: 8 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlprotein1drop
20.1 M1dropNaCl
310 mMTris-HCl1drop
428 %satammonium sulfate1reservoir
52 %MPD1reservoir
60.1 M1reservoirNaCl
70.1 MHEPES1reservoir

-
Data collection

DiffractionMean temperature: 287 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU/MSC RU- / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 15, 1999 / Details: YALE MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.23→50 Å / Num. obs: 19159 / % possible obs: 99 % / Observed criterion σ(I): 0 / Redundancy: 5.3 % / Biso Wilson estimate: 12.8 Å2 / Rmerge(I) obs: 0.148 / Rsym value: 0.148 / Net I/σ(I): 3.4
Reflection shellResolution: 2.23→2.35 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.291 / Mean I/σ(I) obs: 2.1 / Rsym value: 0.291 / % possible all: 96.2
Reflection
*PLUS
Rmerge(I) obs: 0.161
Reflection shell
*PLUS
Lowest resolution: 2.34 Å / % possible obs: 94.9 % / Rmerge(I) obs: 0.339

-
Processing

Software
NameVersionClassification
CNS0.5refinement
MOSFLMdata reduction
SCALAdata scaling
CNS0.5phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1BOS

1bos


Resolution: 2.23→50 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 1625101.21 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.184 1064 5.6 %SHELLS
Rwork0.171 ---
obs0.171 19150 99.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 51.4401 Å2 / ksol: 0.411496 e/Å3
Displacement parametersBiso mean: 26.3 Å2
Baniso -1Baniso -2Baniso -3
1-1.2 Å20 Å22.85 Å2
2--5 Å20 Å2
3----6.19 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.22 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.17 Å0.17 Å
Refinement stepCycle: LAST / Resolution: 2.23→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2700 0 240 80 3020
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
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_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d25
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.7
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.081.5
X-RAY DIFFRACTIONc_mcangle_it1.662
X-RAY DIFFRACTIONc_scbond_it2.052
X-RAY DIFFRACTIONc_scangle_it3.182.5
Refine LS restraints NCSRms dev Biso : 4.81 Å2 / Rms dev position: 0.25 Å / Weight Biso : 1 / Weight position: 5
LS refinement shellResolution: 2.23→2.37 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.212 141 4.5 %
Rwork0.202 2968 -
obs--97.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2STARFISH.PARSTARFISH.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER_REP.TOP
Software
*PLUS
Name: CNS / Version: 0.5 / Classification: refinement
Refinement
*PLUS
σ(F): 0
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg25
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.7

+
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