[English] 日本語
Yorodumi
- PDB-1jqy: HEAT-LABILE ENTEROTOXIN B-PENTAMER WITH LIGAND BMSC-0010 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1jqy
TitleHEAT-LABILE ENTEROTOXIN B-PENTAMER WITH LIGAND BMSC-0010
ComponentsHEAT-LABILE ENTEROTOXIN B CHAIN
KeywordsTOXIN / ENTEROTOXIN / RECEPTOR / LIGAND / B-PENTAMER
Function / homology
Function and homology information


toxin activity / killing of cells of another organism / extracellular region
Similarity search - Function
Heat-labile enterotoxin, B chain / Heat-labile enterotoxin beta chain / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #110 / Enterotoxin / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Chem-A32 / Heat-labile enterotoxin B chain
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.14 Å
AuthorsMerritt, E.A. / Hol, W.G.J.
CitationJournal: Chem.Biol. / Year: 2002
Title: Anchor-based design of improved cholera toxin and E. coli heat-labile enterotoxin receptor binding antagonists that display multiple binding modes.
Authors: Pickens, J.C. / Merritt, E.A. / Ahn, M. / Verlinde, C.L. / Hol, W.G. / Fan, E.
History
DepositionAug 9, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 8, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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
D: HEAT-LABILE ENTEROTOXIN B CHAIN
E: HEAT-LABILE ENTEROTOXIN B CHAIN
F: HEAT-LABILE ENTEROTOXIN B CHAIN
G: HEAT-LABILE ENTEROTOXIN B CHAIN
H: HEAT-LABILE ENTEROTOXIN B CHAIN
L: HEAT-LABILE ENTEROTOXIN B CHAIN
M: HEAT-LABILE ENTEROTOXIN B CHAIN
N: HEAT-LABILE ENTEROTOXIN B CHAIN
O: HEAT-LABILE ENTEROTOXIN B CHAIN
P: HEAT-LABILE ENTEROTOXIN B CHAIN
V: HEAT-LABILE ENTEROTOXIN B CHAIN
W: HEAT-LABILE ENTEROTOXIN B CHAIN
X: HEAT-LABILE ENTEROTOXIN B CHAIN
Y: HEAT-LABILE ENTEROTOXIN B CHAIN
Z: HEAT-LABILE ENTEROTOXIN B CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)183,71329
Polymers177,11315
Non-polymers6,60014
Water19,4921082
1
D: HEAT-LABILE ENTEROTOXIN B CHAIN
E: HEAT-LABILE ENTEROTOXIN B CHAIN
F: HEAT-LABILE ENTEROTOXIN B CHAIN
G: HEAT-LABILE ENTEROTOXIN B CHAIN
H: HEAT-LABILE ENTEROTOXIN B CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,39510
Polymers59,0385
Non-polymers2,3575
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16690 Å2
ΔGint-61 kcal/mol
Surface area19860 Å2
MethodPISA
2
L: HEAT-LABILE ENTEROTOXIN B CHAIN
M: HEAT-LABILE ENTEROTOXIN B CHAIN
N: HEAT-LABILE ENTEROTOXIN B CHAIN
O: HEAT-LABILE ENTEROTOXIN B CHAIN
P: HEAT-LABILE ENTEROTOXIN B CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,9249
Polymers59,0385
Non-polymers1,8864
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16990 Å2
ΔGint-57 kcal/mol
Surface area20040 Å2
MethodPISA
3
V: HEAT-LABILE ENTEROTOXIN B CHAIN
W: HEAT-LABILE ENTEROTOXIN B CHAIN
X: HEAT-LABILE ENTEROTOXIN B CHAIN
Y: HEAT-LABILE ENTEROTOXIN B CHAIN
Z: HEAT-LABILE ENTEROTOXIN B CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,39510
Polymers59,0385
Non-polymers2,3575
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17170 Å2
ΔGint-62 kcal/mol
Surface area20090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.990, 166.006, 74.420
Angle α, β, γ (deg.)90.00, 92.13, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
HEAT-LABILE ENTEROTOXIN B CHAIN


Mass: 11807.539 Da / Num. of mol.: 15
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: ETXB / Plasmid: PROFIT / Production host: Escherichia coli (E. coli) / Strain (production host): MC1061 / References: UniProt: P32890
#2: Chemical
ChemComp-A32 / (3-NITRO-5-(3-MORPHOLIN-4-YL-PROPYLAMINOCARBONYL)PHENYL)-GALACTOPYRANOSIDE / BMSC-0010


Mass: 471.458 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C20H29N3O10
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1082 / 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: 2.26 Å3/Da / Density % sol: 45.68 %
Crystal growMethod: vapor diffusion, sitting drop / pH: 6.5
Details: PEG 3000, NaCl, Tris HCl, pH 6.5, VAPOR DIFFUSION, SITTING DROP
Crystal grow
*PLUS
pH: 7.4
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
12.0 mg/mlprotein1drop
250 mMTris-HCl1droppH7.4
3200 mM1dropNaCl
43 mM1dropNaN3
51 mMEDTA1drop
650 mM1reservoirNaCl
7100 mMTris-HCl1reservoirpH6.5
830 %PEG30001reservoir

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1.0332 Å
DetectorType: CUSTOM-MADE / Detector: CCD / Date: Dec 11, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.14→82 Å / Num. all: 84223 / Num. obs: 84223 / % possible obs: 97.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.6 % / Biso Wilson estimate: 34 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 24
Reflection shellResolution: 2.14→2.22 Å / Redundancy: 4 % / Rmerge(I) obs: 0.205 / Mean I/σ(I) obs: 5.5 / Num. unique all: 7200 / % possible all: 83.3
Reflection
*PLUS
Highest resolution: 2.1 Å / % possible obs: 97 % / Rmerge(I) obs: 0.05
Reflection shell
*PLUS
% possible obs: 83 %

-
Processing

Software
NameVersionClassification
d*TREKdata scaling
SCALEPACKdata scaling
TRUNCATEdata reduction
AMoREphasing
REFMACrefinement
d*TREKdata reduction
CCP4(TRUNCATE)data scaling
RefinementResolution: 2.14→25 Å / Cor.coef. Fo:Fc: 0.921 / SU B: 8.061 / SU ML: 0.21 / σ(F): 0 / ESU R: 0.35 / ESU R Free: 0.26
RfactorNum. reflection% reflection
Rfree0.284 4235 5.031 %
Rwork0.211 --
all-84172 -
obs-84172 -
Refinement stepCycle: LAST / Resolution: 2.14→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12360 0 462 1082 13904
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONp_bond_d0.0150.0213030
X-RAY DIFFRACTIONp_angle_d0.0420.0417592
X-RAY DIFFRACTIONp_planar_d0.0450.053930
X-RAY DIFFRACTIONp_plane_restr0.0120.0210603
X-RAY DIFFRACTIONp_chiral_restr0.1410.151995
X-RAY DIFFRACTIONp_singtor_nbd0.2020.34899
X-RAY DIFFRACTIONp_multtor_nbd0.2540.37662
X-RAY DIFFRACTIONp_xyhbond_nbd0.1870.3572
X-RAY DIFFRACTIONp_xhyhbond_nbd0.3040.385
X-RAY DIFFRACTIONp_planar_tor4.35771590
X-RAY DIFFRACTIONp_staggered_tor18.01152580
X-RAY DIFFRACTIONp_orthonormal_tor14.7920120
X-RAY DIFFRACTIONp_mcbond_it2.5827390
X-RAY DIFFRACTIONp_mcangle_it3.87438817
X-RAY DIFFRACTIONp_scbond_it2.90225640
X-RAY DIFFRACTIONp_scangle_it4.1438775
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.14-2.24250.3134850.235989611333
2.243-2.35540.314930.222944210230
2.355-2.48020.3244820.21585739338
2.48-2.6190.3124120.20676948350
2.619-2.77420.2893580.19969537488
2.774-2.9490.2913340.19761856633
2.949-3.14720.2952960.19954745854
3.147-3.37410.2712660.248415153
3.374-3.63620.2712380.19741764431
3.636-3.94250.2362020.19635873798
3.943-4.30510.2441550.19630543219
4.305-4.74120.2381160.18925702687
4.741-5.27560.2751010.19320882190
5.276-5.94580.323790.22716911770
5.946-6.81090.348760.2712811357
6.811-7.97080.274480.2769721021
7.971-9.60680.28390.299681733
9.607-12.08770.266320.298431485
12.088-16.29610.303150.32273300
16.296-250.28780.41275145
Refinement
*PLUS
Highest resolution: 2.14 Å / Lowest resolution: 25 Å / Rfactor obs: 0.2096 / Rfactor Rfree: 0.2879 / Rfactor Rwork: 0.2096
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.016
X-RAY DIFFRACTIONp_angle_d0.045

+
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