[English] 日本語
Yorodumi
- PDB-6xt3: Crystal structure of E.coli DsbA in complex with 3-(3-(carboxymet... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6xt3
TitleCrystal structure of E.coli DsbA in complex with 3-(3-(carboxymethyl)-6-(3-methoxyphenyl)benzofuran-2-yl)benzoic acid
ComponentsThiol:disulfide interchange protein DsbA
KeywordsOXIDOREDUCTASE/INHIBITOR / Inhibitor / complex / disulfide oxidoreductase / fragments / OXIDOREDUCTASE-OXIDOREDUCTASE INHIBITOR complex / OXIDOREDUCTASE / OXIDOREDUCTASE-INHIBITOR complex
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
COPPER (II) ION / Chem-VED / Thiol:disulfide interchange protein DsbA
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.99 Å
AuthorsWang, G. / Heras, B.
Funding support Australia, 1items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)GNT1099151 Australia
CitationJournal: Bioorg.Med.Chem. / Year: 2021
Title: Elaboration of a benzofuran scaffold and evaluation of binding affinity and inhibition of Escherichia coli DsbA: A fragment-based drug design approach to novel antivirulence compounds.
Authors: Duncan, L.F. / Wang, G. / Ilyichova, O.V. / Dhouib, R. / Totsika, M. / Scanlon, M.J. / Heras, B. / Abbott, B.M.
History
DepositionJul 17, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 11, 2021Provider: repository / Type: Initial release
Revision 1.1Aug 25, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)42,7764
Polymers42,3102
Non-polymers4662
Water4,324240
1
A: Thiol:disulfide interchange protein DsbA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,5572
Polymers21,1551
Non-polymers4021
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Thiol:disulfide interchange protein DsbA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,2192
Polymers21,1551
Non-polymers641
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)118.110, 63.360, 74.694
Angle α, β, γ (deg.)90.000, 125.620, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-384-

HOH

-
Components

#1: Protein Thiol:disulfide interchange protein DsbA


Mass: 21155.025 Da / Num. of mol.: 2
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) / References: UniProt: P0AEG4
#2: Chemical ChemComp-VED / 3-[3-(carboxymethyl)-6-(3-methoxyphenyl)-1-benzofuran-2-yl]benzoic acid


Mass: 402.396 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H18O6 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cu
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 240 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.68 Å3/Da / Density % sol: 54.19 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 11-13% PEG 8000, 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: 0.9537 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Dec 6, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.99→37.28 Å / Num. obs: 31068 / % possible obs: 99.9 % / Redundancy: 4.1 % / CC1/2: 0.998 / Rmerge(I) obs: 0.072 / Rpim(I) all: 0.04 / Rrim(I) all: 0.082 / Net I/σ(I): 13.6 / Num. measured all: 128817 / Scaling rejects: 152
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
1.99-2.0440.891864921820.6220.511.031.299.7
9.1-37.283.60.02812323440.9980.0170.03344.698.1

-
Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
Aimless0.7.4data scaling
PDB_EXTRACT3.25data extraction
iMOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1FVK

1fvk


Resolution: 1.99→34.74 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 26.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2317 1589 5.12 %
Rwork0.2028 29470 -
obs0.2043 31059 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 133.22 Å2 / Biso mean: 46.8608 Å2 / Biso min: 19.46 Å2
Refinement stepCycle: final / Resolution: 1.99→34.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2873 0 47 240 3160
Biso mean--68.42 48.25 -
Num. residues----376
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022979
X-RAY DIFFRACTIONf_angle_d0.3644053
X-RAY DIFFRACTIONf_dihedral_angle_d10.595402
X-RAY DIFFRACTIONf_chiral_restr0.035445
X-RAY DIFFRACTIONf_plane_restr0.002531
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 11 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.99-2.050.32691190.321326502769
2.05-2.120.35981490.295826842833
2.12-2.210.28211640.270426282792
2.21-2.310.29491620.268926582820
2.31-2.430.28461630.229426382801
2.43-2.580.29391430.233927052848
2.58-2.780.23681140.220826872801
2.78-3.060.28341430.2126882831
3.06-3.50.21441680.191126602828
3.51-4.410.18611320.162527102842
4.42-34.740.17731320.173727622894
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)
11.0638-0.33621.34933.67641.95894.06320.11660.3119-0.1697-0.2435-0.00580.17140.04760.3993-0.05490.3217-0.0697-0.0330.33-0.07740.318431.1124-9.83091.1692
21.8466-0.29870.55472.29571.25933.4015-0.10290.1139-0.133-0.19580.02530.0932-0.0770.21780.05320.2019-0.03930.00330.2315-0.00940.210533.9521-5.66459.8064
30.6349-0.1034-0.38952.2051-0.961.5456-0.12860.17540.5911-0.6503-0.24910.4232-0.7155-0.33760.37740.5530.1063-0.0350.3536-0.05180.60162.9739.463221.4079
41.49340.28590.02881.15691.82793.69940.05040.0493-0.02420.1362-0.12270.30110.0398-0.17870.12720.3379-0.00360.10150.2441-0.01680.49619.8972-7.880123.5151
52.40850.02652.56526.3161.12924.2851-0.0036-0.12580.5317-0.4114-0.39880.7178-0.023-0.60250.21450.37720.0219-0.0050.3518-0.01540.45972.4853-7.065118.797
65.82260.9366-0.78385.04050.81593.7137-0.12370.25-0.5656-0.7352-0.007-0.614-0.04290.10050.13940.271-0.04940.08130.2449-0.01760.3478.3786-20.748814.8
78.67222.06432.55744.51870.23162.0058-0.65220.5493-0.7102-0.94650.1777-0.10410.6531-0.70440.33840.3805-0.11630.06210.4739-0.08860.261-1.4495-27.497312.294
82.31040.7316-0.14255.73760.95292.831-0.03130.21730.7997-1.0581-0.03930.5666-0.8554-0.65480.08490.50490.142-0.05280.47310.08830.46270.4701-3.30912.9963
96.2993-1.65590.70978.4671-5.49214.91070.2546-0.1373-0.0095-0.6933-0.3161-0.608-0.0720.97980.23630.5734-0.04240.21650.3206-0.02550.503316.33034.926927.1785
102.45442.22530.92493.43550.65645.64440.1179-0.25770.351-0.0411-0.26170.3862-0.28-0.51430.20680.43950.02850.18730.2423-0.09310.62056.5393.508130.7473
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 65 )A1 - 65
2X-RAY DIFFRACTION2chain 'A' and (resid 66 through 188 )A66 - 188
3X-RAY DIFFRACTION3chain 'B' and (resid 1 through 21 )B1 - 21
4X-RAY DIFFRACTION4chain 'B' and (resid 22 through 49 )B22 - 49
5X-RAY DIFFRACTION5chain 'B' and (resid 50 through 65 )B50 - 65
6X-RAY DIFFRACTION6chain 'B' and (resid 66 through 114 )B66 - 114
7X-RAY DIFFRACTION7chain 'B' and (resid 115 through 128 )B115 - 128
8X-RAY DIFFRACTION8chain 'B' and (resid 129 through 161 )B129 - 161
9X-RAY DIFFRACTION9chain 'B' and (resid 162 through 170 )B162 - 170
10X-RAY DIFFRACTION10chain 'B' and (resid 171 through 188 )B171 - 188

+
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://pdbjlvh1.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