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- PDB-6pg1: Crystal Structure of EcDsbA in a complex with unpurified reaction... -

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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 ...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
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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

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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


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


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


Mass: 18.015 Da / Num. of mol.: 264 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

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

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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

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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

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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 )

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