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- PDB-7s1f: Crystal structure of E.coli DsbA in complex with compound MIPS-00... -

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Basic information

Entry
Database: PDB / ID: 7s1f
TitleCrystal structure of E.coli DsbA in complex with compound MIPS-0001886 (compound 38)
ComponentsThiol:disulfide interchange protein DsbA
KeywordsOXIDOREDUCTASE/OXIDOREDUCTASE inhibitor / thioredoxin fold / thiol-disulfide oxidoreductase / inhibitor / DsbA / OXIDOREDUCTASE / OXIDOREDUCTASE-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 / Thioredoxin-like superfamily
Similarity search - Domain/homology
Chem-5VB / COPPER (II) ION / Thiol:disulfide interchange protein DsbA
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.76 Å
AuthorsHeras, B. / Scanlon, M.J. / Martin, J.L. / Caria, S.
Funding support Australia, 1items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)GNT455860 Australia
CitationJournal: Chemrxiv / Year: 2022
Title: Fluoromethylketone-fragment conjugates designed as covalent modifiers of EcDsbA are atypical substrates
Authors: Bradley, C.D. / Whitehouse, R.L. / Rimmer, K. / Williams, M. / Heras, B. / Caria, S. / Ilyichova, O. / Vazirani, M. / Mohanty, B. / Harper, J. / Scanlon, M.J. / Simpson, J.S.
History
DepositionSep 2, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 8, 2023Provider: repository / Type: Initial release
Revision 1.1Apr 3, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Oct 16, 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)42,7856
Polymers42,3102
Non-polymers4754
Water6,539363
1
A: Thiol:disulfide interchange protein DsbA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,4102
Polymers21,1551
Non-polymers2551
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)21,3744
Polymers21,1551
Non-polymers2193
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)116.131, 63.985, 74.333
Angle α, β, γ (deg.)90.000, 126.100, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-453-

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 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P0AEG4
#2: Chemical ChemComp-5VB / 1-[(3-thiophen-3-ylphenyl)methyl]-3~{H}-pyrrol-2-one


Mass: 255.335 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H13NOS / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cu
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 363 / 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: 2.65 Å3/Da / Density % sol: 53.64 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: 11-13% PEG 8000, 5-7.5% glycerol, 1 mM 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: 0.95369 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Dec 2, 2011
RadiationMonochromator: DOUBLE SI WITH SAGITTALY BENT SECOND CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95369 Å / Relative weight: 1
ReflectionResolution: 1.51→60.06 Å / Num. all: 43413 / Num. obs: 43413 / % possible obs: 99.3 % / Redundancy: 3.9 % / Biso Wilson estimate: 21.62 Å2 / Rpim(I) all: 0.025 / Rrim(I) all: 0.049 / Rsym value: 0.042 / Net I/av σ(I): 15.415 / Net I/σ(I): 20.3 / Num. measured all: 169127
Reflection shellResolution: 1.51→1.76 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.397 / Mean I/σ(I) obs: 2 / Num. unique obs: 6326 / Rpim(I) all: 0.229 / Rsym value: 0.397 / % possible all: 99.8

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å56.49 Å
Translation2.5 Å56.49 Å

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Processing

Software
NameVersionClassification
SCALA3.3.20data scaling
PHASER2.3.0phasing
PHENIXdev_1760refinement
PDB_EXTRACT3.15data extraction
Cootmodel building
Blu-Icedata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: DsbA wt

Resolution: 1.76→56.493 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 18.9 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.2014 2206 5.08 %
Rwork0.1612 41200 -
obs0.1632 43406 99.19 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 101.39 Å2 / Biso mean: 28.6006 Å2 / Biso min: 9.34 Å2
Refinement stepCycle: final / Resolution: 1.76→56.493 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2956 0 26 363 3345
Biso mean--43.77 36.87 -
Num. residues----376
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0123109
X-RAY DIFFRACTIONf_angle_d1.2474210
X-RAY DIFFRACTIONf_chiral_restr0.061453
X-RAY DIFFRACTIONf_plane_restr0.006549
X-RAY DIFFRACTIONf_dihedral_angle_d14.9881141
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.76-1.79830.23811310.20322571X-RAY DIFFRACTION100
1.7983-1.84010.24811510.20782601X-RAY DIFFRACTION100
1.8401-1.88620.29651490.20582545X-RAY DIFFRACTION100
1.8862-1.93720.28051320.21312570X-RAY DIFFRACTION99
1.9372-1.99420.21431240.18412582X-RAY DIFFRACTION100
1.9942-2.05850.23161260.18112586X-RAY DIFFRACTION99
2.0585-2.13210.2451420.17712531X-RAY DIFFRACTION98
2.1321-2.21750.17841480.15722533X-RAY DIFFRACTION100
2.2175-2.31840.21961390.16352544X-RAY DIFFRACTION98
2.3184-2.44060.17571320.1622580X-RAY DIFFRACTION100
2.4406-2.59360.21861220.16322592X-RAY DIFFRACTION100
2.5936-2.79380.18921560.15682574X-RAY DIFFRACTION99
2.7938-3.07490.20211380.16492588X-RAY DIFFRACTION100
3.0749-3.51980.19531280.15242603X-RAY DIFFRACTION99
3.5198-4.43430.17721490.13562561X-RAY DIFFRACTION98
4.4343-56.4930.18411390.15282639X-RAY DIFFRACTION98
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)
10.52390.03810.58041.7499-1.05351.46340.1053-0.1749-0.12030.3382-0.00460.0007-0.0505-0.2408-0.08450.2290.0257-0.02460.20630.03560.1747-30.3898-9.7688-0.4605
21.0941-0.1870.27370.9415-0.26731.5401-0.1015-0.04070.04420.03880.08860.0916-0.0359-0.20940.00570.13920.0526-0.01690.1398-0.00220.1134-36.5494-1.6569-16.8232
30.7448-0.10860.03182.2137-0.69161.31890.0602-0.2369-0.05550.3294-0.0626-0.3056-0.158-0.0218-0.00670.2282-0.001-0.04030.2050.05730.1952-26.4299-13.3653.9815
40.8898-0.4375-0.02411.4236-1.06491.54670.0942-0.0450.21960.14560.06-0.2765-0.57280.3633-0.02390.305-0.05640.06010.2126-0.0330.2586-5.88510.5573-19.8239
54.24030.9251-1.20811.4585-0.90762.05810.0070.1254-0.0439-0.3104-0.0394-0.32770.21090.2458-0.05760.25240.03890.1140.15370.01360.3036-5.8559-6.1738-30.6317
61.59460.5746-0.78332.4373-1.61513.62510.12810.36540.3224-0.0422-0.1033-0.4892-0.12070.47340.02610.18470.03370.03060.38750.00760.3126-0.7042-6.7234-18.8707
72.0851-0.2045-0.9231.4868-0.28630.6929-0.03680.059-0.2586-0.0228-0.06730.07720.0769-0.00280.06850.14490.0557-0.01030.19350.00060.1645-8.0125-20.9628-14.741
82.9742-0.29361.22360.5607-0.64882.254-0.2332-0.1857-0.4470.1838-0.0053-0.11850.24790.2915-0.05120.15290.1979-0.00450.36260.0010.19911.608-27.9057-12.0953
92.1917-0.9478-0.75183.060.7051.8665-0.0054-0.40330.43040.38720.0876-0.6169-0.09760.5058-0.15750.2223-0.0327-0.1150.4417-0.11330.29264.5758-10.398-8.374
102.56521.1942-0.47491.8039-2.05922.80980.2284-0.06220.71270.38020.1439-0.3942-0.98120.5609-0.48820.3482-0.10170.09980.2601-0.08020.4376-3.24642.7336-15.9791
110.64881.05780.17452.83080.67960.18860.03860.01730.18310.24160.07770.2665-0.2494-0.1436-0.27430.47070.0960.28540.16520.1180.4763-15.23475.3562-26.4997
121.2703-0.5955-0.68782.1276-0.34262.93190.3039-0.0250.5016-0.09120.0808-0.3507-0.36750.35650.1970.3622-0.04860.30240.10490.09030.4643-5.07994.179-30.0526
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 65 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 66 through 145 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 146 through 188 )A0
4X-RAY DIFFRACTION4chain 'B' and (resid 1 through 38 )B0
5X-RAY DIFFRACTION5chain 'B' and (resid 39 through 49 )B0
6X-RAY DIFFRACTION6chain 'B' and (resid 50 through 65 )B0
7X-RAY DIFFRACTION7chain 'B' and (resid 66 through 114 )B0
8X-RAY DIFFRACTION8chain 'B' and (resid 115 through 128 )B0
9X-RAY DIFFRACTION9chain 'B' and (resid 129 through 144 )B0
10X-RAY DIFFRACTION10chain 'B' and (resid 145 through 161 )B0
11X-RAY DIFFRACTION11chain 'B' and (resid 162 through 170 )B0
12X-RAY DIFFRACTION12chain 'B' and (resid 171 through 188 )B0

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