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- PDB-6whd: Crystal structure of E.coli DsbA in complex with diaryl ether ana... -

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Basic information

Entry
Database: PDB / ID: 6whd
TitleCrystal structure of E.coli DsbA in complex with diaryl ether analogue 2
ComponentsThiol:disulfide interchange protein DsbA
KeywordsOXIDOREDUCTASE/INHIBITOR / Inhibitor / Complex / OXIDOREDUCTASE / oxidoreductase-oxidoreductase inhibitor complex / 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 / 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 / [4-(4-cyano-3-methylphenoxy)phenyl]acetic acid / Thiol:disulfide interchange protein DsbA
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.99 Å
AuthorsWang, G. / Heras, B.
Funding support Australia, 1items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)GNT1099151 Australia
CitationJournal: J.Med.Chem. / Year: 2020
Title: Rapid Elaboration of Fragments into Leads by X-ray Crystallographic Screening of Parallel Chemical Libraries (REFiLX).
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
DepositionApr 8, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 24, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 22, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.name
Revision 1.2Oct 18, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
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)42,9085
Polymers42,3102
Non-polymers5983
Water4,810267
1
A: Thiol:disulfide interchange protein DsbA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,4222
Polymers21,1551
Non-polymers2671
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)21,4863
Polymers21,1551
Non-polymers3312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)116.770, 64.500, 74.210
Angle α, β, γ (deg.)90.000, 125.890, 90.000
Int Tables number5
Space group name H-MC121

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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 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0AEG4
#2: Chemical ChemComp-KFS / [4-(4-cyano-3-methylphenoxy)phenyl]acetic acid


Mass: 267.279 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H13NO3 / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 267 / 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: 2.68 Å3/Da / Density % sol: 54.03 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.1
Details: 11-13% PEG8000, 5-7.5% glycerol, 1mM CuCl2, 100 mM sodium cacodylate

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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: Nov 10, 2016
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: 1.99→53.29 Å / Num. obs: 30747 / % possible obs: 99.9 % / Redundancy: 4 % / CC1/2: 0.997 / Rmerge(I) obs: 0.069 / Rpim(I) all: 0.04 / Rrim(I) all: 0.079 / Net I/σ(I): 10.3 / Num. measured all: 121459 / Scaling rejects: 100
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
1.99-2.0440.51861221460.8490.2920.5892.399.9
9.12-53.293.80.02613013420.9990.0150.0324.598.4

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
Aimless0.7.1data scaling
PDB_EXTRACT3.25data extraction
MOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1FVK

1fvk


Resolution: 1.99→34.61 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 24.37 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2208 1526 4.97 %
Rwork0.1793 29208 -
obs0.1814 30734 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 129.94 Å2 / Biso mean: 41.3313 Å2 / Biso min: 13.49 Å2
Refinement stepCycle: final / Resolution: 1.99→34.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2896 0 65 267 3228
Biso mean--57.13 43.7 -
Num. residues----376
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013078
X-RAY DIFFRACTIONf_angle_d0.9094171
X-RAY DIFFRACTIONf_dihedral_angle_d10.5413
X-RAY DIFFRACTIONf_chiral_restr0.053449
X-RAY DIFFRACTIONf_plane_restr0.006543
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 11 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.99-2.050.27411480.239426562804
2.05-2.130.25351120.225626502762
2.13-2.210.28711270.205326462773
2.21-2.310.20951190.202226652784
2.31-2.440.25361460.189926112757
2.44-2.590.21761240.19926712795
2.59-2.790.24191360.199926612797
2.79-3.070.25791480.19926222770
3.07-3.510.21751590.179126482807
3.51-4.420.21071340.146526792813
4.42-34.610.18551730.159226992872
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)
11.61590.29341.44575.32672.89132.2830.11480.2131-0.1195-0.299-0.071-0.0632-0.02310.05480.03740.243-0.0369-0.00280.2074-0.00930.189130.6121-9.87930.7471
21.92010.6280.48912.26641.13154.8323-0.10780.06630.0367-0.09470.1012-0.15380.12530.32420.03110.144-0.0146-0.01720.13760.02350.172535.7981-2.076713.1167
32.79611.0196-0.53786.63711.13373.82280.04430.1416-0.0713-0.0878-0.02210.366-0.2348-0.164-0.04950.27720.0344-0.09170.2244-0.02820.212424.7507-17.7422-3.6601
41.07571.46790.16463.3086-0.04044.0559-0.0998-0.04370.4936-0.8716-0.1335-0.1125-1.0406-1.20380.12220.80270.37590.04290.8031-0.0230.66620.83378.932719.7188
53.02180.1247-0.15754.21690.90785.4864-0.04940.2141-0.1952-0.3196-0.13140.0127-0.0616-0.78270.21990.2346-0.00050.01630.3009-0.05410.188910.4819-8.648618.9668
61.46550.8299-2.47611.6838-0.33625.0878-0.3344-0.1957-0.25140.7563-0.21070.75810.5763-0.41480.53750.4313-0.02570.14060.3249-0.07380.41825.9667-6.177630.4545
73.984-1.0279-0.58284.71270.43392.12810.3242-0.3740.3184-0.0548-0.33150.4299-0.0956-0.27720.06330.2589-0.13270.00530.4633-0.07190.28564.1107-14.195716.58
84.54772.3172-0.33115.1392-0.56853.1197-0.0943-0.1276-0.9179-0.13080.0019-0.10180.1433-0.48020.07980.2168-0.09280.00630.3948-0.00590.25536.2014-26.549112.9881
95.79033.7625-0.08476.59691.07725.24770.02840.47970.3929-0.87660.07641.3321-0.5661-1.0303-0.16630.43940.1581-0.09150.60.08060.4776-4.0734-9.98398.0423
101.07070.1597-2.02876.23152.75485.29850.37220.26740.4523-0.7934-0.11640.1696-1.4144-0.8935-0.10230.67530.1820.19460.35940.04830.50777.23423.463719.3274
118.6909-1.72742.96396.1441-1.38785.70260.8267-0.12350.6241-0.3164-0.49330.2088-0.7591-0.8385-0.16510.48880.15280.19360.377-0.05320.46145.29123.522229.6485
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 161 )A66 - 161
3X-RAY DIFFRACTION3chain 'A' and (resid 162 through 188 )A162 - 188
4X-RAY DIFFRACTION4chain 'B' and (resid 1 through 21 )B1 - 21
5X-RAY DIFFRACTION5chain 'B' and (resid 22 through 38 )B22 - 38
6X-RAY DIFFRACTION6chain 'B' and (resid 39 through 49 )B39 - 49
7X-RAY DIFFRACTION7chain 'B' and (resid 50 through 97 )B50 - 97
8X-RAY DIFFRACTION8chain 'B' and (resid 98 through 128 )B98 - 128
9X-RAY DIFFRACTION9chain 'B' and (resid 129 through 145 )B129 - 145
10X-RAY DIFFRACTION10chain 'B' and (resid 146 through 170 )B146 - 170
11X-RAY DIFFRACTION11chain 'B' and (resid 171 through 188 )B171 - 188

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