[English] 日本語
Yorodumi
- PDB-1s5c: Cholera holotoxin with an A-subunit Y30S mutation, Crystal form 1 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1s5c
TitleCholera holotoxin with an A-subunit Y30S mutation, Crystal form 1
Components
  • Cholera enterotoxin, A chain
  • cholera enterotoxin B-subunit
KeywordsTRANSFERASE / TOXIN / cholera toxin / heat-labile enterotoxin / ADP ribose transferases / AB5 toxins
Function / homology
Function and homology information


host cell surface binding / galactose binding / positive regulation of tyrosine phosphorylation of STAT protein / glycosyltransferase activity / Transferases; Glycosyltransferases; Pentosyltransferases / catalytic complex / nucleotidyltransferase activity / toxin activity / periplasmic space / lipid binding ...host cell surface binding / galactose binding / positive regulation of tyrosine phosphorylation of STAT protein / glycosyltransferase activity / Transferases; Glycosyltransferases; Pentosyltransferases / catalytic complex / nucleotidyltransferase activity / toxin activity / periplasmic space / lipid binding / host cell plasma membrane / extracellular space / extracellular region / membrane
Similarity search - Function
Heat-labile enterotoxin, A chain / Heat-labile enterotoxin alpha chain / Heat-Labile Enterotoxin; Chain A / Heat-Labile Enterotoxin, subunit A / Heat-labile enterotoxin, B chain / Heat-labile enterotoxin beta chain / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #110 / Enterotoxin / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Alpha-Beta Complex ...Heat-labile enterotoxin, A chain / Heat-labile enterotoxin alpha chain / Heat-Labile Enterotoxin; Chain A / Heat-Labile Enterotoxin, subunit A / Heat-labile enterotoxin, B chain / Heat-labile enterotoxin beta chain / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #110 / Enterotoxin / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Alpha-Beta Complex / Beta Barrel / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Cholera enterotoxin subunit A / Cholera enterotoxin subunit B
Similarity search - Component
Biological speciesVibrio cholerae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsO'Neal, C.J. / Amaya, E.I. / Jobling, M.G. / Holmes, R.K. / Hol, W.G.
CitationJournal: Biochemistry / Year: 2004
Title: Crystal structures of an intrinsically active cholera toxin mutant yield insight into the toxin activation mechanism
Authors: O'Neal, C.J. / Amaya, E.I. / Jobling, M.G. / Holmes, R.K. / Hol, W.G.
History
DepositionJan 20, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 6, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 23, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Cholera enterotoxin, A chain
D: cholera enterotoxin B-subunit
E: cholera enterotoxin B-subunit
F: cholera enterotoxin B-subunit
G: cholera enterotoxin B-subunit
H: cholera enterotoxin B-subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,2927
Polymers85,2696
Non-polymers231
Water1,69394
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15600 Å2
ΔGint-70 kcal/mol
Surface area27410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.818, 85.199, 71.255
Angle α, β, γ (deg.)90.00, 104.48, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Cholera enterotoxin, A chain / NAD(+)--diphthamide ADP- ribosyltransferase / Cholera enterotoxin A subunit


Mass: 27152.875 Da / Num. of mol.: 1 / Mutation: Y30S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae (bacteria) / Gene: CTXA, TOXA, VC1457 / Plasmid: pEIA154 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P01555, NAD+-diphthamide ADP-ribosyltransferase
#2: Protein
cholera enterotoxin B-subunit


Mass: 11623.267 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae (bacteria) / Gene: CTXB, TOXB, VC1456 / Plasmid: pEIA154 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P01556
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 94 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.2 Å3/Da / Density % sol: 43.65 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: PEG 2000mme, MES, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 1.0414 Å
DetectorType: CUSTOM-MADE / Detector: CCD / Date: Apr 24, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0414 Å / Relative weight: 1
ReflectionResolution: 2.5→19.96 Å / Num. all: 23503 / Num. obs: 23503 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Rsym value: 0.106 / Net I/σ(I): 12.2
Reflection shellResolution: 2.5→2.59 Å / Mean I/σ(I) obs: 2.5 / Num. unique all: 2357 / Rsym value: 0.484 / % possible all: 98.7

-
Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 1LTG, 3CHB

1ltg

3chb


Resolution: 2.5→19.96 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.885 / SU B: 11.12 / SU ML: 0.248 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.338 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26172 1208 5.1 %RANDOM
Rwork0.19542 ---
all0.19882 22291 --
obs0.19882 22291 98.89 %-
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: 16.802 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å2-0.04 Å2
2---0.01 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.5→19.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5612 0 1 94 5707
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0215734
X-RAY DIFFRACTIONr_bond_other_d0.0030.024973
X-RAY DIFFRACTIONr_angle_refined_deg1.2151.9287784
X-RAY DIFFRACTIONr_angle_other_deg0.873311565
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8775722
X-RAY DIFFRACTIONr_chiral_restr0.070.2868
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.026470
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021114
X-RAY DIFFRACTIONr_nbd_refined0.1760.31194
X-RAY DIFFRACTIONr_nbd_other0.1950.35920
X-RAY DIFFRACTIONr_nbtor_other0.0840.53308
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2090.5196
X-RAY DIFFRACTIONr_metal_ion_refined0.080.52
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1020.337
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1940.3105
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2450.511
X-RAY DIFFRACTIONr_mcbond_it0.86933623
X-RAY DIFFRACTIONr_mcangle_it1.42545812
X-RAY DIFFRACTIONr_scbond_it1.36542111
X-RAY DIFFRACTIONr_scangle_it2.17861972
LS refinement shellResolution: 2.5→2.56 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.297 81
Rwork0.236 1568
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)
14.85720.61031.83340.91640.39662.4556-0.02070.25430.37210.11120.15170.2376-0.19770.3746-0.1310.0677-0.030.07290.0969-0.01370.160827.509150.161837.287
2-1.2436-2.5024-2.82945.86122.13921.57580.1862-0.2391-0.03470.256-0.131-0.072-0.65540.1717-0.05520.12370.02550.02320.1825-0.04480.086322.878639.634550.2792
31.13620.8612-0.26381.0263-0.38081.4230.04610.05660.15970.12640.08930.0832-0.06570.0127-0.13550.06040.03060.03280.118-0.02080.121919.869843.426339.6357
40.99680.6897-2.90420.1139-0.87846.3171-0.0264-0.1093-0.0958-0.07380.01440.04330.09840.14080.01190.12120.07750.04270.1840.01980.097734.527332.546532.9032
51.1830.21520.99812.0059-0.71481.4382-0.0679-0.09330.0209-0.0057-0.0245-0.0609-0.00150.070.09240.06630.0118-0.00710.1164-0.01930.103559.425435.666128.1031
62.30640.59050.40721.30110.35031.74130.0972-0.1098-0.12210.00190.0245-0.04790.15690.0359-0.12170.11970.0087-0.0260.06520.03670.0847.159618.823620.8257
70.9827-0.41410.38512.4017-0.14120.53150.0042-0.02390.0718-0.1097-0.01260.07970.1098-0.01630.00840.1029-0.02950.0230.12210.00940.060833.640726.6195.5
81.5219-0.03780.53923.43720.22971.3745-0.05160.0198-0.0276-0.10780.0344-0.1904-0.0884-0.05590.01720.06490.00020.06120.10240.02190.064338.023647.90322.7548
92.2106-0.66820.94462.0199-0.23882.6727-0.23920.10980.22170.19050.0063-0.3428-0.29030.02780.23290.0908-0.0309-0.08340.01210.040.16254.227653.230516.3289
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 251 - 25
2X-RAY DIFFRACTION2AA37 - 4937 - 49
3X-RAY DIFFRACTION3AA51 - 18851 - 188
4X-RAY DIFFRACTION4AA196 - 234196 - 234
5X-RAY DIFFRACTION5DB1 - 1031 - 103
6X-RAY DIFFRACTION6EC1 - 1031 - 103
7X-RAY DIFFRACTION7FD1 - 1031 - 103
8X-RAY DIFFRACTION8GE1 - 1031 - 103
9X-RAY DIFFRACTION9HF1 - 1031 - 103

+
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