[English] 日本語
Yorodumi
- PDB-3ziw: Clostridium perfringens enterotoxin, D48A mutation and N-terminal... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3ziw
TitleClostridium perfringens enterotoxin, D48A mutation and N-terminal 37 residues deleted
ComponentsHEAT-LABILE ENTEROTOXIN B CHAIN
KeywordsTOXIN / BETA PORE-FORMING-TOXIN / CYTOTOXICITY MUTANT
Function / homology
Function and homology information


toxin activity / extracellular region
Similarity search - Function
Jelly Rolls - #1050 / Proaerolysin; Chain A, domain 3 - #20 / Proaerolysin; Chain A, domain 3 / Clostridium enterotoxin / Clostridium enterotoxin / Beta Complex / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Heat-labile enterotoxin B chain
Similarity search - Component
Biological speciesCLOSTRIDIUM PERFRINGENS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 1.9 Å
AuthorsYelland, T. / Naylor, C.E. / Savva, C.G. / Basak, A.K.
Citation
Journal: J.Mol.Biol. / Year: 2014
Title: Structure of a C. Perfringens Enterotoxin Mutant in Complex with a Modified Claudin-2 Extracellular Loop 2
Authors: Yelland, T.S. / Naylor, C.E. / Bagoban, T. / Savva, C.G. / Moss, D.S. / Mcclane, B.A. / Blasig, I.E. / Popoff, M. / Basak, A.K.
#1: Journal: J.Mol.Biol. / Year: 2011
Title: Structure of the Food-Poisoning Clostridium Perfringens Enterotoxin Reveals Similarity to the Aerolysin-Like Pore-Forming Toxins.
Authors: Briggs, D.C. / Naylor, C.E. / Smedley III, J.G. / Lukoyanova, N. / Robertson, S. / Moss, D.S. / Mcclane, B.A. / Basak, A.K.
History
DepositionJan 14, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 29, 2014Provider: repository / Type: Initial release
Revision 1.1Jul 23, 2014Group: Database references
Revision 1.2Aug 27, 2014Group: Database references
Revision 1.3May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_site
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_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: HEAT-LABILE ENTEROTOXIN B CHAIN
B: HEAT-LABILE ENTEROTOXIN B CHAIN
C: HEAT-LABILE ENTEROTOXIN B CHAIN
D: HEAT-LABILE ENTEROTOXIN B CHAIN
E: HEAT-LABILE ENTEROTOXIN B CHAIN
F: HEAT-LABILE ENTEROTOXIN B CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)192,83220
Polymers188,8806
Non-polymers3,95314
Water30,2471679
1
A: HEAT-LABILE ENTEROTOXIN B CHAIN
B: HEAT-LABILE ENTEROTOXIN B CHAIN
C: HEAT-LABILE ENTEROTOXIN B CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,41610
Polymers94,4403
Non-polymers1,9767
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7640 Å2
ΔGint-41.8 kcal/mol
Surface area45900 Å2
MethodPISA
2
D: HEAT-LABILE ENTEROTOXIN B CHAIN
E: HEAT-LABILE ENTEROTOXIN B CHAIN
F: HEAT-LABILE ENTEROTOXIN B CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,41610
Polymers94,4403
Non-polymers1,9767
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6740 Å2
ΔGint-34.9 kcal/mol
Surface area45700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)190.660, 128.020, 136.430
Angle α, β, γ (deg.)90.00, 133.81, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.49256, 0.6421, 0.58745), (-0.75604, 0.01861, -0.65426), (-0.43103, -0.7664, 0.47629)-39.33351, -8.97458, -2.94058
2given(0.04453, 0.02759, 0.99863), (0.0348, -0.99905, 0.02605), (0.9984, 0.03359, -0.04544)-47.60131, 49.07594, 47.67242
3given(0.54859, -0.71358, 0.43572), (-0.67144, -0.06546, 0.73816), (-0.49821, -0.69751, -0.51504)-29.58477, 24.87885, 18.61177
4given(-0.44899, -0.74608, 0.49171), (0.73607, 0.00315, 0.6769), (0.50657, 0.66585, 0.54775)-51.27238, 56.61276, 8.47377
5given(-0.49705, -0.73909, -0.45463), (0.63739, 0.04453, -0.76925), (0.58879, -0.67213, 0.44896)-28.81607, 21.71605, 18.78045

-
Components

#1: Protein
HEAT-LABILE ENTEROTOXIN B CHAIN


Mass: 31479.953 Da / Num. of mol.: 6 / Fragment: RESIDUES 38-319 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CLOSTRIDIUM PERFRINGENS (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P01558
#2: Chemical
ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400


Mass: 282.331 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1679 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsD48A MUTATION AND N-TERMINAL 37 RESIDUES DELETED, AND 34GAMG37 INSTEAD OF NATIVE NSNL DUE TO HIS- ...D48A MUTATION AND N-TERMINAL 37 RESIDUES DELETED, AND 34GAMG37 INSTEAD OF NATIVE NSNL DUE TO HIS-TAG REMOVAL SCAR.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.9 Å3/Da / Density % sol: 58 % / Description: NONE
Crystal growpH: 6 / Details: 25 % PEG 1500, 0.1 M SPG BUFFER, PH 6.0

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.0332
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 29, 2011 / Details: MIRRORS
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 186226 / % possible obs: 99.1 % / Observed criterion σ(I): 0 / Redundancy: 7.3 % / Biso Wilson estimate: 39.28 Å2 / Rmerge(I) obs: 0.15 / Net I/σ(I): 7.42
Reflection shellResolution: 1.9→1.94 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.86 / Mean I/σ(I) obs: 1.26 / % possible all: 93.1

-
Processing

Software
NameVersionClassification
BUSTER2.10.0refinement
XDSdata reduction
XSCALEdata scaling
BUSTERphasing
RefinementMethod to determine structure: OTHER
Starting model: NONE

Resolution: 1.9→49.23 Å / Cor.coef. Fo:Fc: 0.9602 / Cor.coef. Fo:Fc free: 0.9549 / SU R Cruickshank DPI: 0.116 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.12 / SU Rfree Blow DPI: 0.108 / SU Rfree Cruickshank DPI: 0.107
RfactorNum. reflection% reflectionSelection details
Rfree0.1956 9298 5.01 %RANDOM
Rwork0.1749 ---
obs0.176 185455 99.96 %-
Displacement parametersBiso mean: 49.11 Å2
Baniso -1Baniso -2Baniso -3
1-1.6522 Å20 Å2-3.5142 Å2
2--2.535 Å20 Å2
3----4.1872 Å2
Refine analyzeLuzzati coordinate error obs: 0.264 Å
Refinement stepCycle: LAST / Resolution: 1.9→49.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13253 0 185 1679 15117
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0113860HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.0918819HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d4814SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes377HARMONIC2
X-RAY DIFFRACTIONt_gen_planes2005HARMONIC5
X-RAY DIFFRACTIONt_it13860HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.77
X-RAY DIFFRACTIONt_other_torsion15.56
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1866SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact16694SEMIHARMONIC4
LS refinement shellResolution: 1.9→1.95 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2006 643 4.69 %
Rwork0.1929 13062 -
all0.1932 13705 -
obs--99.96 %
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)
10.75830.46010.12772.1601-0.04671.2082-0.1822-0.1170.02440.1445-0.00120.1181-0.175-0.0860.1834-0.02840.02110.0054-0.088-0.0052-0.0005-30.545539.1998-11.1735
21.47050.8275-0.33531.96980.11921.2171-0.03-0.09190.0014-0.029-0.09820.09290.371-0.24950.12810.0058-0.13760.1653-0.0597-0.05290.0296-53.49226.3979-11.4415
30.8859-0.5172-0.48631.08340.17561.2949-0.0769-0.0164-0.0403-0.11780.0311-0.14080.05910.16430.0458-0.058-0.03650.0725-0.0435-0.0179-0.009-5.335122.2498-24.81
42.1008-0.70130.06192.30130.59143.3058-0.3927-0.63540.08360.48050.3263-0.0598-0.1744-0.0090.0665-0.00360.1769-0.0240.0395-0.0409-0.1788-15.519339.1629.4292
51.71860.36010.35992.6194-0.51650.62550.0970.0833-0.40440.0850.0359-0.50030.06190.1069-0.1329-0.07280.0292-0.0289-0.1087-0.080.0642-58.99048.586418.867
61.85360.4091-0.18462.622-0.73581.9808-0.07990.37460.3303-0.44230.031-0.3251-0.14950.05590.0489-0.0172-0.03340.1103-0.04430.0581-0.0508-61.20540.3471-5.013
70.90730.49790.41241.0810.1211.9515-0.08870.23820.0492-0.1540.12910.0539-0.0659-0.0325-0.0404-0.04410.0154-0.0278-0.0025-0.0022-0.1012-79.215634.643912.3122
81.71950.38060.42562.34440.10661.9732-0.0057-0.27980.19320.3463-0.0364-0.0652-0.41590.08950.0420.08180.0043-0.0395-0.0815-0.0569-0.1534-68.625151.907246.4919
91.7440.1393-0.16021.05090.53661.26670.096-0.2315-0.02340.1348-0.03610.0438-0.0464-0.0272-0.0598-0.00950.00920.0017-0.03110.0252-0.1202-72.132926.59244.1064
104.436-0.3159-0.43561.9730.35631.15310.121-0.1167-0.6020.04310.1815-0.49970.040.5065-0.3025-0.20750.0605-0.08910.0265-0.14980.1041-37.98829.570333.6647
111.90230.0159-0.04281.3602-0.04581.11830.07040.09420.1218-0.1686-0.00230.263-0.0065-0.3063-0.0681-0.0517-0.0346-0.008-0.06170.0084-0.048-37.405712.5088-30.6288
123.15060.49230.00352.9138-0.70941.56830.072-0.3995-0.5971-0.1596-0.2296-0.61410.29540.31390.1576-0.10130.02970.0465-0.07280.10870.0827-1.9164-3.3117-22.3359
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{A|34 - 193}
2X-RAY DIFFRACTION2{A|194 - 319}
3X-RAY DIFFRACTION3{B|34 - 193}
4X-RAY DIFFRACTION4{B|194 - 319}
5X-RAY DIFFRACTION5{C|34 - 193}
6X-RAY DIFFRACTION6{C|194 - 319}
7X-RAY DIFFRACTION7{D|34 - 193}
8X-RAY DIFFRACTION8{D|194 - 319}
9X-RAY DIFFRACTION9{E|34 - 193}
10X-RAY DIFFRACTION10{E|194 - 319}
11X-RAY DIFFRACTION11{F|34 - 193}
12X-RAY DIFFRACTION12{F|194 - 319}

+
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