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- PDB-6pbi: Crystal Structure of EcDsbA in a complex with purified morpholine 8 -

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Basic information

Entry
Database: PDB / ID: 6pbi
TitleCrystal Structure of EcDsbA in a complex with purified morpholine 8
ComponentsThiol:disulfide interchange protein DsbA
KeywordsOXIDOREDUCTASE/INHIBITOR / DISULFIDE OXIDOREDUCTASE / REDOX PROTEIN / DSBA / 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-O6Y / Thiol:disulfide interchange protein DsbA
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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 13, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 6, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 11, 2020Group: Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / pdbx_struct_conn_angle / struct_conn
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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry
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

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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)42,7104
Polymers42,3102
Non-polymers4002
Water5,513306
1
A: Thiol:disulfide interchange protein DsbA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,4912
Polymers21,1551
Non-polymers3361
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)117.734, 64.624, 74.404
Angle α, β, γ (deg.)90.000, 125.783, 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-447-

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) / References: UniProt: P0AEG4
#2: Chemical ChemComp-O6Y / 2-methyl-4-{4-[2-(morpholin-4-yl)-2-oxoethyl]phenoxy}benzonitrile


Mass: 336.384 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H20N2O3 / 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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 306 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 54.67 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: 25-35 % PEG MME 2000, 100-300 mM KBr

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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: Jun 21, 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: 1.9→34.79 Å / Num. obs: 35587 / % possible obs: 99.2 % / Redundancy: 4.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.04 / Rpim(I) all: 0.036 / Rrim(I) all: 0.054 / Χ2: 1 / Net I/σ(I): 17.1
Reflection shellResolution: 1.9→1.94 Å / Redundancy: 4 % / Rmerge(I) obs: 0.593 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 2191 / CC1/2: 0.753 / Rpim(I) all: 0.517 / Rrim(I) all: 0.789 / Χ2: 0.98 / % possible all: 96

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Processing

Software
NameVersionClassification
PHENIX1.14_3211refinement
XDSdata reduction
Aimless1.11.12data scaling
PHASER2.8.2phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1DSB

1dsb


Resolution: 1.9→34.79 Å / SU ML: 0.2294 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.8154
RfactorNum. reflection% reflection
Rfree0.2283 1737 4.88 %
Rwork0.1905 --
obs0.1924 35578 99.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 42.11 Å2
Refinement stepCycle: LAST / Resolution: 1.9→34.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2870 0 26 306 3202
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00683010
X-RAY DIFFRACTIONf_angle_d0.79784099
X-RAY DIFFRACTIONf_chiral_restr0.0441449
X-RAY DIFFRACTIONf_plane_restr0.0049539
X-RAY DIFFRACTIONf_dihedral_angle_d6.0832707
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.960.31031180.27882792X-RAY DIFFRACTION97.36
1.96-2.020.27971410.25212821X-RAY DIFFRACTION99.93
2.02-2.090.27531470.24032803X-RAY DIFFRACTION99.9
2.09-2.170.30561370.2242834X-RAY DIFFRACTION99.93
2.17-2.270.26041550.21382807X-RAY DIFFRACTION100
2.27-2.390.27481540.21192844X-RAY DIFFRACTION100
2.39-2.540.28721710.21062763X-RAY DIFFRACTION99.83
2.54-2.740.28081320.21682873X-RAY DIFFRACTION99.9
2.74-3.010.2481220.20262858X-RAY DIFFRACTION99.73
3.01-3.450.21881590.19242802X-RAY DIFFRACTION98.8
3.45-4.350.19081400.15662788X-RAY DIFFRACTION97.31
4.35-34.790.18091610.1612856X-RAY DIFFRACTION97.86
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)
11.55656565173-0.3645127384330.9630815058472.463429962491.753576333372.175493676490.07423133256540.311993638152-0.050067466905-0.319197831118-0.01630623386090.116613508657-0.0518215373230.145438308873-0.008446198011890.280641436492-0.021596949224-0.0314217283130.20264334634-0.01993534053720.19187500868629.1256378704-7.38718411961-1.6943176593
29.39022379667-2.88451693092-4.81529399445.31528577681.383504855587.790276049960.160821483256-0.484347930001-0.5346023475720.495524053907-0.08960995958280.001698133447280.3562450249690.4645535318020.01990300134450.32940322565-0.0465399961146-0.0377931159360.250521128526-0.006664184109780.22388245560430.946322724-18.00029343945.62767587801
31.329589072071.519185815980.4193125240724.114886353841.85513619513.73785413306-0.1548252053120.15876912653-0.470978904625-0.2292443845860.331469073212-0.4301363728410.2046380729660.433083643578-0.175759243420.1871082124950.003762525509570.01247511126570.218703271759-0.05707905496630.3018292803835.9070826808-6.183498692754.29348261033
42.209467123340.7800265678410.1177894094322.157122076960.1835293807883.34349262139-0.0375231409397-0.1247361046780.07323574370040.081674637417-0.00828466193507-0.1411801291510.1925520189890.311552927340.04073657021580.2100274942840.0243323211843-0.03165921857450.221721134333-0.004570484298610.21490609334737.1879494165-0.27399216116516.7069121078
53.891992125610.351151903412-0.6011363464546.23244327741.681021698375.95208504242-0.2209838943470.6386322541460.0951539550082-0.8560490119470.3647500431010.0178283160232-0.261414723804-0.0114693640922-0.09346851946290.270366410541-0.0822553560902-0.02368026576220.3127045272790.007709574864950.21459718332231.2016355812-4.99256841855-4.20405208452
62.573915857490.974678081423-0.8267282686532.25436472882-0.8943942954592.45959969974-0.08482401669830.07500424380570.009397866364630.06566139276470.1217827849610.0255778293759-0.0586803783901-0.123250484787-0.05439971320820.3021403384480.0279817252561-0.05212765742710.215553392738-0.04400820710960.22657467046724.6183011457-17.1967940868-2.84983796392
71.2583587017-0.618794835664-0.8937529720781.49007365684-0.1709983852280.9417406558830.6886644529320.5694362943680.413217707332-1.09315257-0.3379999855280.0806619522184-0.861213471178-0.582202296382-0.02020596434711.149919856750.5227363563030.3107121325260.7374215406980.04543018867810.7097478834382.5867833674610.435291698920.6470446522
81.160707832690.6621039999330.8774715933782.700406770261.675292340854.275730823050.09339402795150.1668697642080.2298064051820.0298304533319-0.2181458704880.437824480744-0.0864219461454-0.592002810480.0240238638250.318300315210.01586364705020.05637680760290.337486464119-0.02908746205710.3648944015996.90168357321-6.5886481346821.6619209535
93.488170667120.65818027875-1.167029084482.020811240150.0577674716661.42515665511-0.00654038182289-0.171803652268-0.142612848346-0.0827549281374-0.1025432880460.174609161704-0.028853313764-0.1890161718570.105473321940.253321912029-0.041802585468-0.01783872189210.374346701751-0.004408003213350.2964773284076.34380467386-21.405555206714.248033569
101.502963931020.2742730879991.312091312523.824546451541.730270739873.034796879760.101567715342-0.05083704062890.670923647822-0.700106368127-0.2036782683990.718294590356-0.919562062546-0.8078990089080.1373151540090.6682482502890.2791790061120.04756846085680.6876256704060.09912968752790.5393658464680.264002669331-2.7746653916812.4588936066
112.252239686930.00594075204324-0.047762941264.61637732415-4.371618974836.294380325290.4476401180660.3641561951060.0735513839531-0.603016807108-0.359794766677-0.417336915164-0.4260616649590.6801206055150.01061742919580.9077361004110.1100517142050.4039819565780.3830905336340.008981444047490.62649860962815.80212561546.2424096005426.6270371204
125.200183344010.8018510581841.409939352823.81011025546-0.5407874947684.327055023970.4821967985630.1899129496360.422157910139-0.185144001549-0.396280539350.301755728103-0.710572510772-0.5928288857160.01664782148240.5098437969840.1442198122420.2179234704720.374273052194-0.06327080289870.5239992095525.964675793274.8211823928430.014773174
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 38 )
2X-RAY DIFFRACTION2chain 'A' and (resid 39 through 49 )
3X-RAY DIFFRACTION3chain 'A' and (resid 50 through 65 )
4X-RAY DIFFRACTION4chain 'A' and (resid 66 through 145 )
5X-RAY DIFFRACTION5chain 'A' and (resid 146 through 161 )
6X-RAY DIFFRACTION6chain 'A' and (resid 162 through 188 )
7X-RAY DIFFRACTION7chain 'B' and (resid 1 through 21 )
8X-RAY DIFFRACTION8chain 'B' and (resid 22 through 65 )
9X-RAY DIFFRACTION9chain 'B' and (resid 66 through 128 )
10X-RAY DIFFRACTION10chain 'B' and (resid 129 through 161 )
11X-RAY DIFFRACTION11chain 'B' and (resid 162 through 170 )
12X-RAY DIFFRACTION12chain 'B' and (resid 171 through 188 )

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