[English] 日本語
Yorodumi
- PDB-6pg1: Crystal Structure of EcDsbA in a complex with unpurified reaction... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6pg1
TitleCrystal Structure of EcDsbA in a complex with unpurified reaction product F1 (methylpiperazinone 6)
ComponentsThiol:disulfide interchange protein DsbA
KeywordsOXIDOREDUCTASE/INHIBITOR / DISULFIDE OXIDOREDUCTASE / REDOX PROTEIN / OXIDOREDUCTASE-INHIBITOR COMPLEX / REFiLX / 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 / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily ...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-O7P / Thiol:disulfide interchange protein DsbA
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.01 Å
AuthorsIlyichova, O.V. / Bentley, M. / Doak, B. / Scanlon, M.J.
Funding support Australia, 2items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)Project Grant APP1099151 Australia
Australian Research Council (ARC)LIEF LE160100047 Australia
CitationJournal: J.Med.Chem. / Year: 2020
Title: Rapid Elaboration of Fragments into Leads by X-ray Crystallographic Screening of Parallel Chemical Libraries (REFiL X ).
Authors: Bentley, M.R. / Ilyichova, O.V. / Wang, G. / Williams, M.L. / Sharma, G. / Alwan, W.S. / Whitehouse, R.L. / Mohanty, B. / Scammells, P.J. / Heras, B. / Martin, J.L. / Totsika, M. / Capuano, ...Authors: Bentley, M.R. / Ilyichova, O.V. / Wang, G. / Williams, M.L. / Sharma, G. / Alwan, W.S. / Whitehouse, R.L. / Mohanty, B. / Scammells, P.J. / Heras, B. / Martin, J.L. / Totsika, M. / Capuano, B. / Doak, B.C. / Scanlon, M.J.
History
DepositionJun 23, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 1, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 11, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
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

-
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)42,7995
Polymers42,3102
Non-polymers4893
Water4,756264
1
A: Thiol:disulfide interchange protein DsbA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,5182
Polymers21,1551
Non-polymers3631
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)21,2813
Polymers21,1551
Non-polymers1262
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)117.996, 64.410, 74.433
Angle α, β, γ (deg.)90.000, 125.854, 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-426-

HOH

21B-393-

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-O7P / 2-methyl-4-{4-[2-(4-methyl-3-oxopiperazin-1-yl)-2-oxoethyl]phenoxy}benzonitrile


Mass: 363.410 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H21N3O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CU / COPPER (II) ION / Copper


Mass: 63.546 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cu
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C2H6O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 264 / 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: 2.71 Å3/Da / Density % sol: 54.6 %
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: Apr 17, 2018
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: 2→47.82 Å / Num. obs: 30133 / % possible obs: 98.8 % / Redundancy: 4.1 % / Biso Wilson estimate: 36.94 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.054 / Rpim(I) all: 0.048 / Rrim(I) all: 0.072 / Net I/σ(I): 9.7
Reflection shellResolution: 2→2.06 Å / Redundancy: 4 % / Rmerge(I) obs: 0.603 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 2125 / CC1/2: 0.782 / Rpim(I) all: 0.522 / Rrim(I) all: 0.8 / % possible all: 95

-
Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1FVK

1fvk


Resolution: 2.01→32.21 Å / SU ML: 0.268 / Cross valid method: FREE R-VALUE / σ(F): 0.32 / Phase error: 28.6061
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2644 959 3.23 %Random selection
Rwork0.2109 28699 --
obs0.2126 29658 97.34 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 49.54 Å2
Refinement stepCycle: LAST / Resolution: 2.01→32.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2888 0 32 264 3184
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00213053
X-RAY DIFFRACTIONf_angle_d0.51624151
X-RAY DIFFRACTIONf_chiral_restr0.037448
X-RAY DIFFRACTIONf_plane_restr0.0039581
X-RAY DIFFRACTIONf_dihedral_angle_d4.17962458
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.01-2.110.31821030.3044077X-RAY DIFFRACTION97.19
2.11-2.240.31731210.2784196X-RAY DIFFRACTION99.52
2.24-2.420.29221450.26134178X-RAY DIFFRACTION99.68
2.42-2.660.28261470.2624154X-RAY DIFFRACTION99.15
2.66-3.040.30231610.23754094X-RAY DIFFRACTION97.95
3.04-3.830.26291660.19093970X-RAY DIFFRACTION94.73
3.83-32.210.2161160.16734030X-RAY DIFFRACTION93.27
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)
11.677018423660.1094649561951.15549439554.280814617212.451354457893.303843291430.03969318994540.335074619089-0.135439698521-0.23119059588-0.0127453061079-0.0849124408735-0.06029864624950.145213204923-0.01314843869850.199151804831-0.015939426338-0.01470457559380.244437082546-0.02530274057790.2124814692131.2537590355-2.96990570710.91173444283
23.538251012431.302037280290.5965937431951.92713736191-0.2276192215073.048243764660.0110958313178-0.06230551833140.01118680945730.17893248869-0.106941690841-0.0464507636540.1650065584890.01487269103130.09490508012730.276079258833-0.0044887656594-0.02292398312980.215432652428-0.009654071678020.1857928733833.54109133764.3778037707318.9716757701
31.414621237591.283541301581.318640808053.506372443772.053858076242.74937867118-0.1392674188670.191434007473-0.0288162921004-0.2367566771060.174948871878-0.01483942719860.01351199368510.351614680563-0.02864424052040.2132560085840.0396291792798-0.009222378120880.2829145388570.01047708189080.20428420712133.9360925047-0.5446941851333.10320574499
41.723064851350.5367305872990.5523354425343.434977699842.334242331113.910530519540.4090319040450.4336639201340.188845479167-0.416225967126-0.3424142720480.757101672684-0.796074457933-0.846004130357-0.0366771115410.4854082358030.1039234798390.09381949844020.525384963237-0.01732886451120.492301371835.955155508744.4333133101921.3560954378
56.057474791941.18463944286-1.083143503643.166791914240.2959494113291.482814347660.0433510776816-0.30349128538-0.282220833839-0.128473942566-0.1604110496270.166545208048-0.0725956012048-0.2014232982080.09494159641080.298235931642-0.05563011676930.003667814024790.414629367148-0.02163093214060.2555814645986.46342976249-15.10827786614.2652019075
62.44153002832-0.1222148217141.501201410974.770286468592.057122594422.92279210578-0.242158664477-0.2860148050480.762454746816-0.4644011343430.08022190514480.867811472691-0.911859983832-0.8190180046910.2457994760580.6784740706910.299296292360.02189759361990.7801689342690.1017026519010.5020188463590.2315025335483.3617860788912.1034507274
76.81594599771.61544330428-0.3298656999366.40799737047-1.488221506176.773775424140.587976644973-0.05383871827880.397409648172-0.850961576308-0.9128145823220.0204657431855-0.918160677728-0.5720323967420.1760158461110.6465079439390.1670229354670.1591913296950.377940004247-0.1081446048120.4542371941669.3259289907111.430624868429.1571828179
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 65 )
2X-RAY DIFFRACTION2chain 'A' and (resid 66 through 114 )
3X-RAY DIFFRACTION3chain 'A' and (resid 115 through 188 )
4X-RAY DIFFRACTION4chain 'B' and (resid 1 through 65 )
5X-RAY DIFFRACTION5chain 'B' and (resid 66 through 128 )
6X-RAY DIFFRACTION6chain 'B' and (resid 129 through 161 )
7X-RAY DIFFRACTION7chain 'B' and (resid 162 through 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