[English] 日本語
Yorodumi
- PDB-6pvy: E.coli DsbA in complex with benzofuran compound 26 ([6-(3-methoxy... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6pvy
TitleE.coli DsbA in complex with benzofuran compound 26 ([6-(3-methoxyphenoxy)-1-benzofuran-3-yl]acetic acid)
ComponentsThiol:disulfide interchange protein DsbA
KeywordsOXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR / Inhibitor / complex / disulfide oxidoreductase / fragments / 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 / Glutaredoxin / Glutaredoxin ...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 / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
COPPER (II) ION / Chem-OZG / DI(HYDROXYETHYL)ETHER / Thiol:disulfide interchange protein DsbA
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.74 Å
AuthorsWang, G. / Heras, B.
Funding support Australia, 1items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)GNT1099151 Australia
CitationJournal: Molecules / Year: 2019
Title: The Fragment-Based Development of a Benzofuran Hit as a New Class of Escherichia coli DsbA Inhibitors.
Authors: Duncan, L.F. / Wang, G. / Ilyichova, O.V. / Scanlon, M.J. / Heras, B. / Abbott, B.M.
History
DepositionJul 21, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 25, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 7, 2020Group: Database references / Category: citation / Item: _citation.title
Revision 1.2Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Oct 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
B: Thiol:disulfide interchange protein DsbA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,9347
Polymers42,3102
Non-polymers6245
Water4,756264
1
A: Thiol:disulfide interchange protein DsbA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,6384
Polymers21,1551
Non-polymers4833
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Thiol:disulfide interchange protein DsbA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,2973
Polymers21,1551
Non-polymers1422
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)117.317, 63.895, 74.461
Angle α, β, γ (deg.)90.000, 125.840, 90.000
Int Tables number5
Space group name H-MC121

-
Components

-
Protein , 1 types, 2 molecules AB

#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

-
Non-polymers , 5 types, 269 molecules

#2: Chemical ChemComp-OZG / [6-(3-methoxyphenoxy)-1-benzofuran-3-yl]acetic acid


Mass: 298.290 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H14O5 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Cu
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 264 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.69 Å3/Da / Density % sol: 54.27 %
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
PH range: 6.0-6.3

-
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: Mar 23, 2019
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95366 Å / Relative weight: 1
ReflectionResolution: 1.74→48.45 Å / Num. obs: 45582 / % possible obs: 98.8 % / Redundancy: 3.5 % / Biso Wilson estimate: 33.17 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.072 / Rpim(I) all: 0.043 / Rrim(I) all: 0.084 / Net I/σ(I): 6.6 / Num. measured all: 161630 / Scaling rejects: 20
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
1.74-1.773.20.538739122940.8280.3480.6431.491.7
9.02-48.453.40.06210433070.9790.0390.07410.386.7

-
Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
Aimless0.7.3data scaling
PDB_EXTRACT3.25data extraction
iMOSFLM7.2.2data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1FVK

1fvk


Resolution: 1.74→34.63 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 27.33
RfactorNum. reflection% reflection
Rfree0.2253 2417 5.31 %
Rwork0.1925 --
obs0.1943 45558 98.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 130.67 Å2 / Biso mean: 47.3 Å2 / Biso min: 22.97 Å2
Refinement stepCycle: final / Resolution: 1.74→34.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2873 0 68 264 3205
Biso mean--92.48 49.43 -
Num. residues----376
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042973
X-RAY DIFFRACTIONf_angle_d0.6124037
X-RAY DIFFRACTIONf_chiral_restr0.041444
X-RAY DIFFRACTIONf_plane_restr0.004525
X-RAY DIFFRACTIONf_dihedral_angle_d9.8521742
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 17

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7365-1.77190.35111160.31092373248993
1.7719-1.81040.30731340.27152562269699
1.8104-1.85250.30561490.25912538268799
1.8525-1.89890.29141270.25032538266599
1.8989-1.95020.26811320.24012569270199
1.9502-2.00760.21021140.23252569268399
2.0076-2.07240.28021450.22962520266599
2.0724-2.14640.2331550.220525442699100
2.1464-2.23240.26571700.221125322702100
2.2324-2.33390.26051480.218425592707100
2.3339-2.4570.23241460.21432542268899
2.457-2.61080.25611290.22082562269199
2.6108-2.81230.25731720.20942521269399
2.8123-3.09520.25121260.20592558268499
3.0952-3.54270.23361600.18542543270399
3.5427-4.46190.18551420.1512543268598
4.4619-34.63670.18051520.16672568272097
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)
1-0.0423-0.58291.33625.85864.02374.97870.00380.3026-0.0261-0.15450.03540.0342-0.05650.2996-0.02510.267-0.0936-0.00580.3849-0.05820.295330.7373-9.69780.9308
23.21681.10040.01252.53230.14024.954-0.17130.11140.0177-0.00970.0855-0.12450.06390.32620.080.2037-0.0183-0.02390.2178-0.01320.235536.9356-1.42616.962
32.0651.0197-0.03443.12851.63684.82690.01760.29770.0308-0.53840.030.5277-0.1260.378-0.03740.3377-0.0055-0.06310.4268-0.0830.35927.38-13.3044-3.9271
40.8190.4965-0.4964.43342.79263.70290.31050.18540.432-0.5064-0.29640.4057-0.6496-0.6911-0.02670.37440.08690.05440.363-0.00070.45345.6133-2.320121.5995
53.2016-0.279-3.13626.80951.94215.15380.0211-0.0674-0.4552-0.2387-0.1229-0.085-0.0211-0.00440.12850.2297-0.0352-0.02040.27460.00220.28018.3416-20.883815.037
65.95812.07770.49962.24881.5912.1129-0.43230.3803-0.7361-0.5432-0.14780.34960.3392-0.64120.54040.3285-0.07320.00620.4738-0.02770.3779-1.3995-27.682612.0695
72.12491.1135-2.38529.2328-3.53583.22220.01811.00930.2362-1.41790.21540.5957-0.7069-1.103-0.14650.60770.2372-0.16090.65920.10810.4696-3.9617-10.05648.3642
86.12660.62262.08894.7303-0.33492.07780.4134-0.10881.3596-1.1324-0.08580.3281-1.5574-0.6723-0.23720.80810.21320.10150.45120.05290.6443.93642.35216.9027
94.20982.47292.36675.9389-1.39353.34270.14910.00180.5237-0.4001-0.2566-0.1182-0.23360.01340.1080.50590.06140.17920.2976-0.04580.53259.15284.152129.3427
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 144 )A66 - 144
3X-RAY DIFFRACTION3chain 'A' and (resid 145 through 188 )A145 - 188
4X-RAY DIFFRACTION4chain 'B' and (resid 1 through 65 )B1 - 65
5X-RAY DIFFRACTION5chain 'B' and (resid 66 through 114 )B66 - 114
6X-RAY DIFFRACTION6chain 'B' and (resid 115 through 128 )B115 - 128
7X-RAY DIFFRACTION7chain 'B' and (resid 129 through 144 )B129 - 144
8X-RAY DIFFRACTION8chain 'B' and (resid 145 through 161 )B145 - 161
9X-RAY DIFFRACTION9chain 'B' and (resid 162 through 188 )B162 - 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://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