[English] 日本語
Yorodumi
- PDB-2vse: Structure and mode of action of a mosquitocidal holotoxin -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2vse
TitleStructure and mode of action of a mosquitocidal holotoxin
ComponentsMOSQUITOCIDAL TOXIN
KeywordsTOXIN / ADP-RIBOSYLTRANSFERASE / LECTIN / RICIN-B-LIKE DOMAIN
Function / homology
Function and homology information


: / Scabin-like / Clostridium botulinum HA-17 domain / Heat-Labile Enterotoxin; Chain A / Heat-Labile Enterotoxin, subunit A / 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 ...: / Scabin-like / Clostridium botulinum HA-17 domain / Heat-Labile Enterotoxin; Chain A / Heat-Labile Enterotoxin, subunit A / 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 / Prokaryotic membrane lipoprotein lipid attachment site profile. / Alpha-Beta Complex / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Biological speciesLYSINIBACILLUS SPHAERICUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsTreiber, N. / Reinert, D.J. / Carpusca, I. / Aktories, K. / Schulz, G.E.
CitationJournal: J.Mol.Biol. / Year: 2008
Title: Structure and Mode of Action of a Mosquitocidal Holotoxin.
Authors: Treiber, N. / Reinert, D.J. / Carpusca, I. / Aktories, K. / Schulz, G.E.
History
DepositionApr 22, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 8, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AL" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AL" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 6-STRANDED BARREL THIS IS REPRESENTED BY A 7-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "AP", "BH" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 7-STRANDED BARREL THIS IS REPRESENTED BY A 8-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "BK" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 5-STRANDED BARREL THIS IS REPRESENTED BY A 6-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: MOSQUITOCIDAL TOXIN
B: MOSQUITOCIDAL TOXIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)195,2616
Polymers194,8142
Non-polymers4474
Water12,178676
1
A: MOSQUITOCIDAL TOXIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,5252
Polymers97,4071
Non-polymers1181
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: MOSQUITOCIDAL TOXIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,7364
Polymers97,4071
Non-polymers3283
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)130.963, 130.963, 396.061
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11A-2108-

HOH

21B-2082-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: GLY / End label comp-ID: GLY / Refine code: 2 / Auth seq-ID: 31 - 866 / Label seq-ID: 2 - 837

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

NCS oper: (Code: given
Matrix: (0.51287, 0.85821, -0.02107), (0.85842, -0.51294, 0.00201), (-0.00908, -0.01912, -0.99978)
Vector: -62.09147, 38.974, 375.45111)

-
Components

#1: Protein MOSQUITOCIDAL TOXIN / MTX HOLOTOXIN


Mass: 97407.227 Da / Num. of mol.: 2 / Fragment: HOLOTOXIN, RESIDUES 30-870
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) LYSINIBACILLUS SPHAERICUS (bacteria) / Strain: SSII-1 / Plasmid: PGEX / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: Q03988
#2: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 676 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsMTX 30-870 WAS USED FOR CRYSTALLIZATION

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.4 Å3/Da / Density % sol: 63.9 %
Description: MODEL FOR RICIN B-TYPE DOMAINS WAS CALCULATED WITH FFAS03 AND SCWRL SERVERS
Crystal growpH: 8.3
Details: 0.1 M TRIS, PH 8.3 3% (W/V) PEG-6000 250 MM KCL 4% MPD

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.918
DetectorType: MARREASEARCH / Detector: CCD / Date: Jul 12, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionResolution: 2.5→75 Å / Num. obs: 87586 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 7.1 % / Rmerge(I) obs: 0.09 / Rsym value: 0.084 / Net I/σ(I): 18.6
Reflection shellResolution: 2.5→2.58 Å / Redundancy: 5 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 3.3 / Rsym value: 0.48 / % possible all: 99.8

-
Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2CB4

2cb4


Resolution: 2.5→74.54 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.912 / SU B: 15.62 / SU ML: 0.183 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.358 / ESU R Free: 0.246 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.234 4379 5 %RANDOM
Rwork0.192 ---
obs0.194 83206 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 49.23 Å2
Baniso -1Baniso -2Baniso -3
1-1.46 Å20.73 Å20 Å2
2--1.46 Å20 Å2
3----2.19 Å2
Refinement stepCycle: LAST / Resolution: 2.5→74.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13480 0 30 676 14186
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.02213846
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2011.91718831
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6351639
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.5325.323774
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.837152273
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.3781562
X-RAY DIFFRACTIONr_chiral_restr0.0890.21988
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0210870
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2010.25992
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3090.29352
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1380.2860
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2770.276
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1790.218
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.3021.58396
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.556213348
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.07236297
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.6464.55483
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
3288tight positional0.040.05
3449medium positional0.210.5
3288tight thermal0.060.5
3449medium thermal0.372
LS refinement shellResolution: 2.5→2.56 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.287 325
Rwork0.266 6173
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)
18.8265-0.37571.0211.72470.10492.66340.26771.8380.1421-0.3596-0.39-0.1171-0.08030.42850.1223-0.24260.05640.01430.47050.0878-0.238952.942184.985145.541
28.9289-0.578-1.72093.3369-0.064.183-0.33260.2693-0.7910.0237-0.0929-0.41050.5330.37720.4255-0.2938-0.02190.08870.15270.0173-0.051783.285372.8281162.5276
36.6759-0.95311.82553.2893-1.61184.4538-0.1037-0.5731-0.15110.13570.18630.150.0889-0.556-0.0826-0.2942-0.0767-0.0030.06050.0068-0.272353.821777.1172177.1795
48.3536-0.7743.91343.3890.58546.9322-0.0749-2.1811-0.01740.45550.20640.1026-0.1529-1.2675-0.1315-0.2509-0.0245-0.00810.4376-0.0217-0.249321.919985.0458169.4579
54.14211.40190.9322.42260.61254.4094-0.05340.01870.26590.08560.0394-0.1617-0.28870.25070.014-0.4046-0.0451-0.0283-0.40280.0038-0.252114.51587.0875139.2204
63.58492.9183-0.74836.8553-1.33813.11760.2668-0.53490.00891.2059-0.4878-0.455-0.52050.47980.2210.2483-0.2954-0.1247-0.071-0.0203-0.12534.941.1682227.8854
76.65564.82832.763111.37342.29425.7036-0.5836-0.26281.7292-0.4643-0.40041.4577-0.7793-0.26790.9840.2705-0.2893-0.2122-0.1143-0.1510.498939.704673.4539210.773
85.34272.02062.34957.8762-0.16464.0814-0.40550.46540.4109-1.15670.28720.2609-0.16350.2390.11830.3292-0.3011-0.0184-0.15050.0178-0.144227.974545.9717196.3545
92.88780.4115-1.74384.4472-0.97215.8275-0.24330.3152-0.1021-0.84240.32590.15070.3025-0.1765-0.08260.0101-0.18070.0111-0.2612-0.015-0.300418.581814.6143204.3613
103.21771.2057-1.03562.8539-0.6624.86820.0742-0.0865-0.0658-0.0419-0.1222-0.3243-0.08950.40370.048-0.4556-0.01980.0087-0.36040.0281-0.250717.0876.9437234.5155
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A31 - 295
2X-RAY DIFFRACTION2A296 - 441
3X-RAY DIFFRACTION3A442 - 581
4X-RAY DIFFRACTION4A582 - 724
5X-RAY DIFFRACTION5A725 - 866
6X-RAY DIFFRACTION6B31 - 295
7X-RAY DIFFRACTION7B296 - 441
8X-RAY DIFFRACTION8B442 - 581
9X-RAY DIFFRACTION9B582 - 725
10X-RAY DIFFRACTION10B726 - 866

+
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