[English] 日本語
Yorodumi
- PDB-3d3x: Crystal structure of botulinum neurotoxin serotype E catalytic do... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3d3x
TitleCrystal structure of botulinum neurotoxin serotype E catalytic domain in complex with SNAP-25 substrate peptide
Components
  • SNAP-25 substrate peptide
  • Type E botulinum toxin
KeywordsHYDROLASE/HYDROLASE SUBSTRATE / BoNT E / SNAP-25 / Enzyme-substrate complex / HYDROLASE / HYDROLASE-HYDROLASE SUBSTRATE COMPLEX
Function / homology
Function and homology information


negative regulation of neurotransmitter secretion / protein transmembrane transporter activity / : / metalloendopeptidase activity / toxin activity / zinc ion binding / extracellular region
Similarity search - Function
Zincin-like / Metalloproteases ("zincins"), catalytic domain like / Clostridium neurotoxin, translocation / Clostridium neurotoxin, Translocation domain / Clostridium neurotoxin, translocation domain / Clostridial neurotoxin zinc protease / Botulinum/Tetanus toxin, catalytic chain / Clostridium neurotoxin, receptor binding N-terminal / Clostridium neurotoxin, receptor-binding C-terminal / Clostridium neurotoxin, C-terminal receptor binding ...Zincin-like / Metalloproteases ("zincins"), catalytic domain like / Clostridium neurotoxin, translocation / Clostridium neurotoxin, Translocation domain / Clostridium neurotoxin, translocation domain / Clostridial neurotoxin zinc protease / Botulinum/Tetanus toxin, catalytic chain / Clostridium neurotoxin, receptor binding N-terminal / Clostridium neurotoxin, receptor-binding C-terminal / Clostridium neurotoxin, C-terminal receptor binding / Clostridium neurotoxin, N-terminal receptor binding / Kunitz inhibitor STI-like superfamily / Concanavalin A-like lectin/glucanase domain superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Botulinum neurotoxin type E
Similarity search - Component
Biological speciesClostridium butyricum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.25 Å
AuthorsAgarwal, R. / Swaminathan, S.
CitationJournal: J.Biol.Chem. / Year: 2008
Title: SNAP-25 substrate peptide (residues 180-183) binds to but bypasses cleavage by catalytically active Clostridium botulinum neurotoxin E.
Authors: Agarwal, R. / Swaminathan, S.
History
DepositionMay 13, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 8, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Structure summary / Version format compliance
Revision 1.2May 2, 2012Group: Source and taxonomy / Structure summary
Revision 1.3Aug 30, 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 / struct_conn / struct_conn_type / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _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_label_seq_id / _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_label_seq_id / _struct_conn_type.id / _struct_ref_seq_dif.details / _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: Type E botulinum toxin
B: Type E botulinum toxin
C: SNAP-25 substrate peptide
D: SNAP-25 substrate peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,34014
Polymers98,4414
Non-polymers89910
Water4,522251
1
A: Type E botulinum toxin
C: SNAP-25 substrate peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,8629
Polymers49,2212
Non-polymers6427
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Type E botulinum toxin
D: SNAP-25 substrate peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,4785
Polymers49,2212
Non-polymers2583
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)89.410, 144.738, 83.303
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

-
Components

#1: Protein Type E botulinum toxin


Mass: 48673.844 Da / Num. of mol.: 2 / Fragment: catalytic domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium butyricum (bacteria) / Strain: NCTC 11219 / Gene: bont/E / Plasmid: pET9c / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) RIPL / References: UniProt: Q9K395
#2: Protein/peptide SNAP-25 substrate peptide


Mass: 546.684 Da / Num. of mol.: 2 / Source method: obtained synthetically
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 251 / 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: 2.74 Å3/Da / Density % sol: 55.07 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: Lithium sulfate, Ammonium sulfate, Na-Citrate, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.008 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 30, 2007 / Details: mirrors
RadiationMonochromator: Si-III / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.008 Å / Relative weight: 1
ReflectionResolution: 2.25→50 Å / Num. all: 49220 / Num. obs: 49220 / % possible obs: 94.5 % / Observed criterion σ(I): 0 / Redundancy: 13.1 % / Biso Wilson estimate: 21.2 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 11.1
Reflection shellResolution: 2.25→2.33 Å / Redundancy: 8.5 % / Rmerge(I) obs: 0.22 / Mean I/σ(I) obs: 3 / Num. unique all: 3439 / % possible all: 67.2

-
Processing

Software
NameVersionClassification
CNS1.1refinement
CBASSdata collection
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: pdb entry 1T3A

1t3a


Resolution: 2.25→33.48 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 90049.52 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.288 1426 3 %RANDOM
Rwork0.235 ---
obs0.235 47715 91.6 %-
all-49220 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 29.2759 Å2 / ksol: 0.326794 e/Å3
Displacement parametersBiso mean: 37.6 Å2
Baniso -1Baniso -2Baniso -3
1-14.79 Å20 Å20 Å2
2---14.24 Å20 Å2
3----0.55 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.42 Å0.32 Å
Luzzati d res low-5 Å
Luzzati sigma a0.34 Å0.33 Å
Refinement stepCycle: LAST / Resolution: 2.25→33.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6586 0 42 251 6879
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d22.9
X-RAY DIFFRACTIONc_improper_angle_d0.95
LS refinement shellResolution: 2.25→2.39 Å / Rfactor Rfree error: 0.028 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.37 177 3.2 %
Rwork0.316 5388 -
obs-49220 65.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2ion.paramcapping.top
X-RAY DIFFRACTION3water_rep.param
X-RAY DIFFRACTION4capping.param

+
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