[English] 日本語
Yorodumi
- PDB-5bp5: Crystal structure of HA17-HA33-IPT -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5bp5
TitleCrystal structure of HA17-HA33-IPT
Components
  • HA-17
  • HA-33
KeywordsPROTEIN BINDING / Botulinum neurotoxin A / Hemagglutinin / IPTG
Function / homology
Function and homology information


Toxicity of botulinum toxin type A (botA) / Toxicity of botulinum toxin type B (botB) / carbohydrate binding
Similarity search - Function
Hemagglutinin component HA-17 / Clostridium botulinum HA-17 domain / Ricin-type beta-trefoil lectin domain-like / Ricin-type beta-trefoil / Lectin domain of ricin B chain profile. / Ricin B, lectin domain / Ricin B-like lectins / Trefoil (Acidic Fibroblast Growth Factor, subunit A) - #50 / Trefoil (Acidic Fibroblast Growth Factor, subunit A) / Trefoil / Mainly Beta
Similarity search - Domain/homology
1-methylethyl 1-thio-beta-D-galactopyranoside / HA-33 / HA-17
Similarity search - Component
Biological speciesClostridium botulinum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.18 Å
AuthorsLee, K. / Lam, K. / Jin, R.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI091823 United States
CitationJournal: Toxicon / Year: 2015
Title: Inhibiting oral intoxication of botulinum neurotoxin A complex by carbohydrate receptor mimics.
Authors: Lee, K. / Lam, K.H. / Kruel, A.M. / Mahrhold, S. / Perry, K. / Cheng, L.W. / Rummel, A. / Jin, R.
History
DepositionMay 27, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 2, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 9, 2015Group: Database references
Revision 1.2Sep 20, 2017Group: Advisory / Author supporting evidence / Derived calculations
Category: pdbx_audit_support / pdbx_struct_oper_list ...pdbx_audit_support / pdbx_struct_oper_list / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Nov 1, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.4Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.name / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.6Dec 27, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: HA-33
C: HA-17
B: HA-33
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,7095
Polymers85,2333
Non-polymers4772
Water3,081171
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4740 Å2
ΔGint-22 kcal/mol
Surface area30870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.868, 118.928, 162.197
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
DetailsTrimer according to gel filtration

-
Components

#1: Protein HA-33 / HA-33 protein / HA33 / HA34 / Non-toxin haemagglutinin HA34


Mass: 34081.656 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium botulinum (bacteria) / Gene: HA-33, ha33, ha34 / Plasmid: pRSFDuet-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-RIL (DE3) / References: UniProt: Q45871
#2: Protein HA-17 / HA-17 protein / HA17 / Ha17 protein / Non-toxin haemagglutinin HA17


Mass: 17069.195 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium botulinum (bacteria) / Gene: ha17, HA-17 / Plasmid: pRSFDuet-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-RIL (DE3) / References: UniProt: Q45878
#3: Sugar ChemComp-IPT / 1-methylethyl 1-thio-beta-D-galactopyranoside / ISOPROPYL-1-BETA-D-THIOGALACTOSIDE / 1-(ISOPROPYLTHIO)-BETA-GALACTOPYRANSIDE / 1-methylethyl 1-thio-beta-D-galactoside / 1-methylethyl 1-thio-D-galactoside / 1-methylethyl 1-thio-galactoside / Isopropyl β-D-1-thiogalactopyranoside


Type: D-saccharide / Mass: 238.301 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H18O5S
IdentifierTypeProgram
isopropyl-1-b-D-thiogalactosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 171 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.99 Å3/Da / Density % sol: 58.93 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 0.1 M MES, 0.1 M magnesium chloride, 5% PEG 8000 / PH range: 6.2

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 21, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.18→47.95 Å / Num. obs: 53512 / % possible obs: 99.5 % / Redundancy: 3.3 % / Net I/σ(I): 15.1

-
Processing

Software
NameVersionClassification
HKL-2000data scaling
REFMAC5.7.0029refinement
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
PHASERphasing
RefinementResolution: 2.18→47.95 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.937 / SU B: 0.002 / SU ML: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.173 / ESU R Free: 0.182
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2385 2711 5.1 %RANDOM
Rwork0.2268 ---
obs0.2274 50625 99.38 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 121.81 Å2 / Biso mean: 53.795 Å2 / Biso min: 26.8 Å2
Baniso -1Baniso -2Baniso -3
1--1.39 Å20 Å20 Å2
2---0.42 Å20 Å2
3---1.8 Å2
Refinement stepCycle: final / Resolution: 2.18→47.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5842 0 30 171 6043
Biso mean--31.92 51.85 -
Num. residues----713
LS refinement shellResolution: 2.18→2.236 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.392 202 -
Rwork0.359 3699 -
all-3901 -
obs--99.36 %

+
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