[English] 日本語
Yorodumi
- PDB-7l76: Crystal Structure of EcDsbA in a complex with 2-(6-Phenylbenzofur... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7l76
TitleCrystal Structure of EcDsbA in a complex with 2-(6-Phenylbenzofuran-3-yl)acetic acid
ComponentsThiol:disulfide interchange protein DsbA
KeywordsOXIDOREDUCTASE/INHIBITOR / DISULFIDE OXIDOREDUCTASE / REDOX PROTEIN / OXIDOREDUCTASE-INHIBITOR COMPLEX / OXIDOREDUCTASE
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 / (6-phenyl-1-benzofuran-3-yl)acetic acid / Thiol:disulfide interchange protein DsbA
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.83 Å
AuthorsIlyichova, O.V. / Scanlon, M.J.
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
DepositionDec 26, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 11, 2021Provider: repository / Type: Initial release
Revision 1.1Aug 25, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Oct 9, 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)42,6264
Polymers42,3102
Non-polymers3162
Water6,269348
1
A: Thiol:disulfide interchange protein DsbA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,4072
Polymers21,1551
Non-polymers2521
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
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
MethodPISA
Unit cell
Length a, b, c (Å)117.513, 64.031, 74.704
Angle α, β, γ (deg.)90.000, 125.820, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11A-449-

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 / Plasmid: B0013 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P0AEG4
#2: Chemical ChemComp-XPV / (6-phenyl-1-benzofuran-3-yl)acetic acid


Mass: 252.265 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C16H12O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CU / COPPER (II) ION


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


Mass: 18.015 Da / Num. of mol.: 348 / 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: 2.71 Å3/Da / Density % sol: 54.61 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 6.1
Details: 11-13 % PEG 8000, 5-7.5% glycerol, 100mM Na Cacodylate pH6.1, 1mM CuCl2

-
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: Jun 17, 2014
RadiationMonochromator: DOUBLE SI WITH SAGITTALY BENT SECOND CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.83→47.64 Å / Num. obs: 39774 / % possible obs: 100 % / Redundancy: 4.2 % / Biso Wilson estimate: 27.19 Å2 / Rmerge(I) obs: 0.051 / Rpim(I) all: 0.028 / Rrim(I) all: 0.059 / Net I/σ(I): 16.3
Reflection shellResolution: 1.83→1.93 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.659 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 5741 / Rpim(I) all: 0.368 / Rrim(I) all: 0.757 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX1.19_4092refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1FVK

1fvk


Resolution: 1.83→37.28 Å / SU ML: 0.2282 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.3419
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2244 1997 5.02 %
Rwork0.1816 37763 -
obs0.1838 39760 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 36.73 Å2
Refinement stepCycle: LAST / Resolution: 1.83→37.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2886 0 20 348 3254
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01753028
X-RAY DIFFRACTIONf_angle_d1.38114119
X-RAY DIFFRACTIONf_chiral_restr0.0819450
X-RAY DIFFRACTIONf_plane_restr0.0102560
X-RAY DIFFRACTIONf_dihedral_angle_d5.259426
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.83-1.880.3591550.30952656X-RAY DIFFRACTION99.96
1.88-1.930.2931120.27782697X-RAY DIFFRACTION99.93
1.93-1.980.33161260.23842724X-RAY DIFFRACTION99.93
1.98-2.050.26281540.2142663X-RAY DIFFRACTION99.89
2.05-2.120.24471280.21572691X-RAY DIFFRACTION100
2.12-2.210.2511480.2152679X-RAY DIFFRACTION99.96
2.21-2.310.27161330.2092692X-RAY DIFFRACTION100
2.31-2.430.25451340.19752694X-RAY DIFFRACTION99.93
2.43-2.580.2751530.19652695X-RAY DIFFRACTION100
2.58-2.780.24971480.18752690X-RAY DIFFRACTION100
2.78-3.060.23871530.18642695X-RAY DIFFRACTION100
3.06-3.50.22811410.1692711X-RAY DIFFRACTION100
3.5-4.410.16691540.14482711X-RAY DIFFRACTION100
4.41-37.280.18131580.15372765X-RAY DIFFRACTION99.97
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)
12.859017507331.19206933265-0.6567536108247.78023461262.126645206251.508090684760.1281319857740.3542480325820.174598327001-1.29492799410.09791141589680.018810865203-0.4756879221331.43847665811-0.1218062694960.550908294743-0.110438564953-0.05929067036650.605178061948-0.02227947321860.25701944610830.8184444689-9.51522086307-11.4902384938
20.5971619382720.8313858441790.5352216499076.678906848153.223887223453.210717129250.03838037189170.213559804081-0.1000171351120.259638759637-0.00338766195559-0.1278929682120.258690283969-0.0370571144912-0.04085237618280.241581747752-0.10105979131-0.02140715043530.307141472708-0.04706286373170.21061531957831.0091957879-10.04213772846.20913787336
34.24402340618-0.245726200785-0.0430975838051.36124944577-0.5609633506133.83484903124-0.09688053058170.0380044804291-0.08571050353470.0394353019369-0.009954967554960.03266537670860.126403689391-0.07906563796670.1200935122620.183466607033-0.0594979378156-0.02430512852770.159443801215-0.01835751151320.13087734440133.2231037262-2.9907411086819.0253583646
45.262371027383.67886324912-3.518466605563.39130712977-3.400111327513.69229986053-0.344254836982-0.243987503867-0.134742187887-0.0294834830663-0.0172515368976-0.5244063558010.5220712516760.8433928774510.4318512573630.268008873430.0138324367389-0.04653382141010.375253607129-0.01913767049160.24085458936144.400993586-1.4297655491323.3548468288
54.25368569796-0.1507721667182.335010348752.54900261042-0.5559134601023.65561115253-0.185249020060.401884862970.11930600893-0.4305762948490.165952555428-0.331612381894-0.09321037937710.7256431822430.1056200716450.27520330805-0.1592155272260.02451933117250.4240439265450.03133338690090.2398362840542.18607735482.786440650675.19722533741
60.3845121689970.980408689370.829183438536.889550728831.561903961312.810288353950.1131830348480.2185720854320.0222602674258-0.353230573553-0.02704975389530.453858911266-0.03688950199950.373296693067-0.08314578466730.2567147416770.0010087147974-0.08024284744230.367709399078-0.08422013758890.24996798206827.1786114647-14.0166608753-3.73009392601
72.431799088441.59645068259-1.310514696715.015487152912.107460964474.207597920120.347570539610.427509030910.544895284922-0.940264873541-0.08848736829180.451379722834-1.13182141723-0.792173242362-0.142826264240.7418695778920.226085626440.106879161770.4422142901380.06140841991870.5225867308092.651860156929.4171086424621.4495268544
83.359161596150.0788920382484-0.9274394821474.181231196793.315913591886.876881829880.2409398200230.2780922615640.222983589283-0.162968478397-0.1895696959410.345613979632-0.338082187919-0.582002218752-0.07225710444230.2371981318340.001255630304610.02040124903510.16947089010.04667084006070.2497284897476.91025654413-7.53709079221.9041765662
98.620450182670.428076474785-2.146281119485.560407323750.8742755311154.443953676220.0878278830629-0.08622064387850.0570473570801-0.144370950962-0.1899807146110.132188779298-0.0848910517789-0.2311128853320.09081182406330.18307326204-0.0546291498334-0.0526570656570.1948302260410.002340206093470.1613841042786.13917236031-18.157055150715.5894441795
109.005951035991.827915876650.4757256236884.885467017450.1019375855014.83457574735-0.4594460692910.0535158491641-0.874222516353-0.1344506671550.159771733044-0.2696004145660.299615317463-0.2136141580330.2433422165620.187887325435-0.03207149378810.01915227989080.194984068644-0.007433313208460.2161925220516.20803109642-26.431594107712.9760426328
114.125785687460.05578443990581.176037271841.639276018680.3111420548373.038639830790.3879860918830.5402667819790.80788219718-0.4951442397580.03893540818510.415218460264-1.05958952584-0.891059564830.03803884145270.4926722907740.2487384624150.01578931260450.5683791967930.1866531029440.4128032100290.227285307413-3.3391283720712.5034491167
120.4072235903340.663314581213-0.9912094832083.94288462511-3.640085372893.846562738320.162103711018-0.04277349902810.238047184298-0.291806238774-0.0624320726658-0.438255510219-0.3896273991030.4977180000950.009761494316110.655257412613-0.0434723117820.3180221625270.247413448764-0.06274713930070.5643849075415.91346768435.1012997220327.309234853
130.4692057116531.653022520170.3441208838496.062197833830.335989408986.865221372960.301135140218-0.04925457725260.404293743966-0.0545358370790.1687377138280.678525539313-0.492386544015-1.00060986104-0.2315097313340.4829516642710.07627228122960.2852939582950.142951493641-0.0534869841750.488518278965.697763025874.0282668944230.4582686803
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 1 through 21 )AA1 - 211 - 21
22chain 'A' and (resid 22 through 65 )AA22 - 6522 - 65
33chain 'A' and (resid 66 through 114 )AA66 - 11466 - 114
44chain 'A' and (resid 115 through 128 )AA115 - 128115 - 128
55chain 'A' and (resid 129 through 145 )AA129 - 145129 - 145
66chain 'A' and (resid 146 through 188 )AA146 - 188146 - 188
77chain 'B' and (resid 1 through 21 )BC1 - 211 - 21
88chain 'B' and (resid 22 through 65 )BC22 - 6522 - 65
99chain 'B' and (resid 66 through 97 )BC66 - 9766 - 97
1010chain 'B' and (resid 98 through 128 )BC98 - 12898 - 128
1111chain 'B' and (resid 129 through 161 )BC129 - 161129 - 161
1212chain 'B' and (resid 162 through 170 )BC162 - 170162 - 170
1313chain 'B' and (resid 171 through 188 )BC171 - 188171 - 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