[English] 日本語
Yorodumi
- PDB-7lsm: Crystal structure of E.coli DsbA in complex with bile salt tauroc... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7lsm
TitleCrystal structure of E.coli DsbA in complex with bile salt taurocholate
ComponentsThiol:disulfide interchange protein DsbA
KeywordsOXIDOREDUCTASE / Inhibitor / complex / antibacterial
Function / homology
Function and homology information


cellular response to antibiotic / protein disulfide isomerase activity / protein-disulfide reductase activity / outer membrane-bounded periplasmic space
Similarity search - Function
Thiol:disulphide interchange protein DsbA/DsbL / : / DSBA-like thioredoxin domain / DSBA-like thioredoxin domain / Thioredoxin, conserved site / Thioredoxin family active site. / Thioredoxin domain profile. / Thioredoxin domain / Thioredoxin-like superfamily
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / TAUROCHOLIC ACID / Thiol:disulfide interchange protein DsbA
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.786 Å
AuthorsWang, G. / Heras, B.
Funding support Australia, 2items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)1144046 Australia
National Health and Medical Research Council (NHMRC, Australia)1099151 Australia
CitationJournal: Chemmedchem / Year: 2022
Title: Selective Binding of Small Molecules to Vibrio cholerae DsbA Offers a Starting Point for the Design of Novel Antibacterials.
Authors: Wang, G. / Mohanty, B. / Williams, M.L. / Doak, B.C. / Dhouib, R. / Totsika, M. / McMahon, R.M. / Sharma, G. / Zheng, D. / Bentley, M.R. / Ka-Yan Chin, Y. / Horne, J. / Chalmers, D.K. / Heras, B. / Scanlon, M.J.
History
DepositionFeb 18, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 29, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 2, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Feb 9, 2022Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.3Mar 30, 2022Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.4Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Thiol:disulfide interchange protein DsbA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,7773
Polymers21,1551
Non-polymers6222
Water3,171176
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)46.800, 50.110, 66.640
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Thiol:disulfide interchange protein DsbA


Mass: 21155.025 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: dsbA, dsf, ppfA, b3860, JW3832 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P0AEG4
#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical ChemComp-TCH / TAUROCHOLIC ACID


Mass: 515.703 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C26H45NO7S / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 176 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.85 Å3/Da / Density % sol: 33.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 11-13% PEG8000, 5-7.5% glycerol, 1 mM copper(II) chloride, 100 mM sodium cacodylate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.95366 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Sep 22, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95366 Å / Relative weight: 1
ReflectionResolution: 1.786→38.3 Å / Num. obs: 15471 / % possible obs: 100 % / Redundancy: 13.9 % / Biso Wilson estimate: 10.18 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.126 / Rpim(I) all: 0.035 / Rrim(I) all: 0.13 / Net I/σ(I): 16.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.79-1.8213.30.257114678640.9790.0730.2678.5100
9.11-38.39.70.10514681520.9980.0330.11118.698.8

-
Processing

Software
NameVersionClassification
Aimless0.5.17data scaling
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.25data extraction
MOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1FVK

1fvk


Resolution: 1.786→34.203 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 19.45 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2072 755 4.89 %
Rwork0.1636 14670 -
obs0.1659 15425 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 53.68 Å2 / Biso mean: 11.2206 Å2 / Biso min: 1.51 Å2
Refinement stepCycle: final / Resolution: 1.786→34.203 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1443 0 52 176 1671
Biso mean--14.98 17.74 -
Num. residues----184
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061526
X-RAY DIFFRACTIONf_angle_d1.2192071
X-RAY DIFFRACTIONf_chiral_restr0.07230
X-RAY DIFFRACTIONf_plane_restr0.005262
X-RAY DIFFRACTIONf_dihedral_angle_d14.312898
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
1.7861-1.92390.24111670.16662852
1.9239-2.11750.21751450.16482889
2.1175-2.42390.23291240.16412931
2.4239-3.05350.22011580.17762924
3.0535-34.2030.17471610.15353074

+
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