[English] 日本語
Yorodumi
- PDB-3boo: Structure of the C. botulinum neurotoxin serotype A with an inhib... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3boo
TitleStructure of the C. botulinum neurotoxin serotype A with an inhibitory peptide bound
Components
  • N-Ac-CRATKML inhibitory peptide
  • Neurotoxin A
KeywordsTOXIN/TOXIN INHIBITOR / botulinum / neurotoxin / metalloprotease / peptidic inhibitor / TOXIN-TOXIN INHIBITOR COMPLEX
Function / homology
Function and homology information


bontoxilysin / host cell presynaptic membrane / host cell cytoplasmic vesicle / host cell cytosol / protein transmembrane transporter activity / metalloendopeptidase activity / toxin activity / host cell plasma membrane / proteolysis / zinc ion binding ...bontoxilysin / host cell presynaptic membrane / host cell cytoplasmic vesicle / host cell cytosol / protein transmembrane transporter activity / metalloendopeptidase activity / toxin activity / host cell plasma membrane / proteolysis / zinc ion binding / extracellular region / membrane
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 / Neutral zinc metallopeptidases, zinc-binding region signature. / Concanavalin A-like lectin/glucanase domain superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Bont/A1 / Botulinum neurotoxin type A
Similarity search - Component
Biological speciesClostridium botulinum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.4 Å
AuthorsSilvaggi, N.R. / Allen, K.N.
CitationJournal: Biochemistry / Year: 2008
Title: Catalytic features of the botulinum neurotoxin A light chain revealed by high resolution structure of an inhibitory peptide complex.
Authors: Silvaggi, N.R. / Wilson, D. / Tzipori, S. / Allen, K.N.
History
DepositionDec 17, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 20, 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 1.2Oct 25, 2017Group: Refinement description / Category: software
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_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Neurotoxin A
B: N-Ac-CRATKML inhibitory peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,7253
Polymers49,6592
Non-polymers651
Water11,025612
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1100 Å2
ΔGint-5.6 kcal/mol
Surface area18710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.046, 66.571, 65.380
Angle α, β, γ (deg.)90.000, 98.630, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Neurotoxin A


Mass: 48793.094 Da / Num. of mol.: 1 / Fragment: LIGHT CHAIN (RESIDUES 1-425)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium botulinum (bacteria) / Gene: BOTA, ATX, BNA / Plasmid: PET-15B / Production host: Escherichia coli (E. coli) / Strain (production host): BL-21(DE3)
References: UniProt: A2I2U2, UniProt: P0DPI1*PLUS, bontoxilysin
#2: Protein/peptide N-Ac-CRATKML inhibitory peptide


Mass: 866.105 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Inhibitory peptide was chemically synthesized
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 612 / 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: 2.17 Å3/Da / Density % sol: 43.3 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.9
Details: 20% PEG 3350, 0.1M AMMONIUM TARTRATE, pH 6.9, vapor diffusion, hanging drop, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12B / Wavelength: 0.95 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 15, 2007
RadiationMonochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95 Å / Relative weight: 1
ReflectionResolution: 1.4→50 Å / Num. all: 83517 / Num. obs: 79759 / % possible obs: 95.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Rmerge(I) obs: 0.055 / Χ2: 0.961 / Net I/σ(I): 20.5
Reflection shellResolution: 1.4→1.45 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.341 / Mean I/σ(I) obs: 2.6 / Num. unique all: 6631 / Χ2: 0.86 / % possible all: 79.6

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACT3.004data extraction
CBASSdata collection
RefinementStarting model: PDB ID 3BOK

3bok


Resolution: 1.4→20.988 Å / FOM work R set: 0.877 / σ(F): 0 / Stereochemistry target values: ML / Details: Riding hydrogen atoms were used in the refinement
RfactorNum. reflection% reflectionSelection details
Rfree0.178 3608 4.99 %RANDOM
Rwork0.148 ---
all0.1567 81939 --
obs0.15 75886 86.54 %-
Solvent computationShrinkage radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 52.922 Å2 / ksol: 0.407 e/Å3
Displacement parametersBiso max: 165.15 Å2 / Biso mean: 22.76 Å2 / Biso min: 7.04 Å2
Baniso -1Baniso -2Baniso -3
1-10.479 Å20 Å25.06 Å2
2---5.216 Å2-0 Å2
3----5.264 Å2
Refinement stepCycle: LAST / Resolution: 1.4→20.988 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3461 0 1 612 4074
Refine LS restraints
Refine-IDTypeDev idealWeight
X-RAY DIFFRACTIONf_angle_d1.1811
X-RAY DIFFRACTIONf_bond_d0.0131
X-RAY DIFFRACTIONf_chiral_restr0.1031
X-RAY DIFFRACTIONf_dihedral_angle_d17.9971
X-RAY DIFFRACTIONf_plane_restr0.0071
X-RAY DIFFRACTIONf_nbd_refined3.7531
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 26

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.4-1.4180.2971030.2091956205964.2
1.418-1.4380.251030.2062010211365.89
1.438-1.4580.2181080.1942103221169.38
1.458-1.480.2531200.1862213233372.48
1.48-1.5030.2181130.1762251236474.86
1.503-1.5280.1961130.172346245976.65
1.528-1.5540.1861290.1682427255679.58
1.554-1.5820.1981370.1662488262581.57
1.582-1.6130.1851370.1652558269584.35
1.613-1.6450.1921340.1642549268384.99
1.645-1.6810.2261440.1572661280586.84
1.681-1.720.1791400.1512639277987.06
1.72-1.7630.1791370.1462672280987.97
1.763-1.8110.1651510.152796294791.15
1.811-1.8640.1841440.1462704284889
1.864-1.9240.1881450.1462786293191.57
1.924-1.9930.1731510.1442831298293.16
1.993-2.0730.1561520.142904305694.97
2.073-2.1670.1791550.1382926308195.98
2.167-2.2810.1661520.1332957310996.88
2.281-2.4240.1761510.1312921307295.76
2.424-2.6110.1671570.1372978313596.73
2.611-2.8730.1731590.1412993315297.95
2.873-3.2870.1751580.1483022318098.24
3.287-4.1360.1551600.1343028318898.06
4.136-20.990.1611550.1412951310693.98
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.0458-0.11560.12070.1890.00780.1494-0.0289-0.02330.01010.145-0.0177-0.1211-0.06540.1360.00010.2279-0.0213-0.00880.1485-0.01560.150522.68341.294834.7514
20.01840.00930.06060.13080.00030.18250.0014-0.02840.07320.07860.08210.28230.0562-0.1233-00.1867-0.01930.01450.1360.0070.186112.7607-1.753531.4289
30.1255-0.06890.02040.1018-0.1187-0.041-0.02370.0755-0.02750.0516-0.02730.260.1693-0.1553-00.1769-0.03670.02010.1686-0.00320.21289.2994-16.980922.2445
40.18-0.02-0.03620.16420.25770.38870.01670.00380.00480.0941-0.0132-0.0314-0.08590.053600.1318-0.0162-0.00270.12630.00320.132221.3737-0.217222.5482
5-0.0184-0.00330.09470.04980.21480.0992-0.0815-0.10310.01050.14050.01910.111-0.2145-0.313300.19880.02970.00540.221-0.01920.1941.88049.328331.7034
60.0166-0.0125-0.03120.0518-0.12910.2457-0.01360.0086-0.02540.0736-0.01790.0346-0.0089-0.0687-00.11-0.00530.00330.141-0.01150.13689.73-2.518420.6904
7-0.0475-0.0470.10630.11980.00050.273-0.01150.0183-0.0037-0.0374-0.00040.00460.0407-0.017800.1141-0.0099-0.00050.1326-0.00510.137219.858-7.99216.8417
8-0.0019-0.18470.05180.1094-0.05940.04910.0930.1482-0.117-0.1991-0.06940.02750.0553-0.0287-0.0010.1233-0.0072-0.04250.1577-0.04480.14319.6611-8.5018-0.9322
90.32430.12030.31370.3447-0.33190.3249-0.09250.017-0.0584-0.07050.13760.1445-0.2383-0.22220.00130.25560.1136-0.00190.24080.0480.16084.000710.86563.9051
100.45440.0478-0.1657-0.1764-0.15050.86170.12260.0260.1434-0.09420.0007-0.1311-0.38170.00090.00230.22420.00420.01660.09860.00760.135813.187213.443612.1673
110.173-0.1903-0.24860.31490.15210.17510.0254-0.0751-0.0015-0.07510.0126-0.1167-0.00310.0528-00.1035-0.02370.00090.1641-0.00330.156933.5444-10.190414.2758
120.1374-0.0445-0.05330.14570.1290.2127-0.05250.1221-0.2019-0.03810.0656-0.11950.15010.03200.1349-0.01280.01350.1705-0.01370.16530.7583-18.862110.1304
130.0036-0.0088-0.00010.00720.01380.012-0.2159-0.0004-0.16690.1342-0.04540.25920.1794-0.1572-0.00010.1817-0.04430.02730.1745-0.03340.195911.3753-13.84397.6429
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsLabel asym-IDLabel seq-ID
1X-RAY DIFFRACTION1chain A and resseq :23A1 - 23
2X-RAY DIFFRACTION2chain A and resseq 24:47A24 - 47
3X-RAY DIFFRACTION3chain A and resseq 48:73A48 - 73
4X-RAY DIFFRACTION4chain A and resseq 74:120A74 - 120
5X-RAY DIFFRACTION5chain A and resseq 121:143A121 - 143
6X-RAY DIFFRACTION6chain A and resseq 144:195A144 - 195
7X-RAY DIFFRACTION7chain A and resseq 196:238A196 - 238
8X-RAY DIFFRACTION8chain A and resseq 239:268A239 - 268
9X-RAY DIFFRACTION9chain A and resseq 269:301A269 - 301
10X-RAY DIFFRACTION10chain A and resseq 302:366A302 - 366
11X-RAY DIFFRACTION11chain A and resseq 367:398A367 - 398
12X-RAY DIFFRACTION12chain A and resseq 399:423A399 - 423
13X-RAY DIFFRACTION13chain BB0 - 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://pdbjlc1.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