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- PDB-4zij: Crystal structure of E.Coli DsbA in complex with 2-(4-iodophenyls... -

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Basic information

Entry
Database: PDB / ID: 4zij
TitleCrystal structure of E.Coli DsbA in complex with 2-(4-iodophenylsulfonamido) benzoic acid
ComponentsThiol:disulfide interchange protein DsbA
KeywordsOXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR / DISULFIDE OXIDOREDUCTASE / REDOX PROTEIN / DSBA / 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 / 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
2-{[(4-iodophenyl)sulfonyl]amino}benzoic acid / Thiol:disulfide interchange protein DsbA
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.78 Å
AuthorsVazirani, M. / Ilyichova, O.V. / Scanlon, M.J.
Funding support Australia, 3items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)1009785 Australia
Australian Research Council (ARC)CE0562063 Australia
Australian Research Council (ARC)FT110100925 Australia
CitationJournal: J.Biomol.Nmr / Year: 2016
Title: Determination of ligand binding modes in weak protein-ligand complexes using sparse NMR data.
Authors: Mohanty, B. / Williams, M.L. / Doak, B.C. / Vazirani, M. / Ilyichova, O. / Wang, G. / Bermel, W. / Simpson, J.S. / Chalmers, D.K. / King, G.F. / Mobli, M. / Scanlon, M.J.
History
DepositionApr 28, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 11, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 9, 2016Group: Database references
Revision 1.2Dec 7, 2016Group: Database references
Revision 1.3Sep 6, 2017Group: Author supporting evidence / Data collection / Database references
Category: citation / diffrn_source / pdbx_audit_support
Item: _citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site / _pdbx_audit_support.funding_organization
Revision 1.4Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Sep 27, 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)42,5174
Polymers42,0522
Non-polymers4652
Water6,972387
1
A: Thiol:disulfide interchange protein DsbA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,4292
Polymers21,0261
Non-polymers4031
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)21,0882
Polymers21,0261
Non-polymers621
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)123.965, 46.982, 62.288
Angle α, β, γ (deg.)90.00, 96.20, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Thiol:disulfide interchange protein DsbA


Mass: 21025.846 Da / Num. of mol.: 2 / Fragment: UNP residues 20-207
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: dsbA, dsf, ppfA, b3860, JW3832 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P0AEG4
#2: Chemical ChemComp-SFQ / 2-{[(4-iodophenyl)sulfonyl]amino}benzoic acid


Mass: 403.192 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H10INO4S
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 387 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.13 Å3/Da / Density % sol: 42.33 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 100-200 mM KBr, 22-27% PEG 2000 MME

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Aug 3, 2013
RadiationMonochromator: Double-crystal Si(111) water-cooled / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.78→46.25 Å / Num. obs: 34294 / % possible obs: 99.6 % / Redundancy: 4 % / Rmerge(I) obs: 0.055 / Net I/σ(I): 15.8
Reflection shellResolution: 1.78→1.88 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.19 / Mean I/σ(I) obs: 5.3 / % possible all: 97.7

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1692)refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
Blu-Icedata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1FVK

1fvk


Resolution: 1.78→41.497 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 21.8 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2171 1728 5.04 %Random selection
Rwork0.1735 ---
obs0.1758 34289 99.55 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.78→41.497 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2907 0 24 387 3318
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063056
X-RAY DIFFRACTIONf_angle_d0.8794157
X-RAY DIFFRACTIONf_dihedral_angle_d15.4191113
X-RAY DIFFRACTIONf_chiral_restr0.036455
X-RAY DIFFRACTIONf_plane_restr0.004545
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.78-1.83250.26491330.1882605X-RAY DIFFRACTION96
1.8325-1.89160.2691390.20372692X-RAY DIFFRACTION100
1.8916-1.95930.25951580.20822713X-RAY DIFFRACTION100
1.9593-2.03770.23141330.19042682X-RAY DIFFRACTION100
2.0377-2.13040.21481410.18562735X-RAY DIFFRACTION100
2.1304-2.24270.26581400.17812695X-RAY DIFFRACTION100
2.2427-2.38320.23451410.18482724X-RAY DIFFRACTION100
2.3832-2.56720.22911680.18512678X-RAY DIFFRACTION100
2.5672-2.82550.23091450.18482737X-RAY DIFFRACTION100
2.8255-3.23430.22881410.18642735X-RAY DIFFRACTION100
3.2343-4.07430.18491590.15392736X-RAY DIFFRACTION100
4.0743-41.50810.1741300.14382829X-RAY DIFFRACTION100
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)
11.5866-0.1276-0.02263.647-1.02141.70330.07020.10830.1354-0.0103-0.08380.078-0.1412-0.10130.00360.1624-0.04-0.01350.15830.03070.1323-19.435528.782313.825
22.29240.5616-0.17781.665-0.471.1786-0.03990.0629-0.0565-0.07690.07220.0796-0.0222-0.1266-0.02480.1276-0.0219-0.00230.1048-0.02010.0763-20.361519.932717.1251
31.1922-2.59862.67715.767-5.87276.06840.141-0.0105-0.2935-0.6790.02140.34050.3448-0.1579-0.04890.1946-0.0267-0.03530.1209-0.02150.23215.6397-4.17956.0752
43.0457-0.1262-0.94953.24010.74392.97350.1011-0.1708-0.03120.1651-0.1013-0.10560.17460.10580.00030.1064-0.0411-0.01850.12520.00780.11138.026911.519714.5814
52.9071-2.8451-0.18493.13460.06485.47960.2582-0.1111-0.176-0.2268-0.30720.13730.10610.04210.00870.1415-0.04630.00190.1604-0.0160.210811.063115.593412.3175
64.7328-0.0196-0.4061.91810.23141.66490.0501-0.37050.0154-0.0202-0.1093-0.02310.0093-0.01460.05370.1146-0.06860.01950.1433-0.02690.10719.481924.70919.2051
72.5034-0.2702-0.96411.1659-0.66852.04020.0871-0.54860.36160.0902-0.2010.0047-0.3197-0.10450.11010.1463-0.0750.00970.2717-0.1080.188310.448732.116123.1623
84.57683.60282.8914.89132.64371.8878-0.12490.5028-0.0502-0.76330.2999-0.3358-0.57390.4469-0.10450.2549-0.06990.07480.23760.00840.13514.614624.55495.3953
93.5385-1.2547-0.02244.1609-0.41553.28480.1473-0.1532-0.41610.3707-0.14040.02660.2515-0.0841-0.00870.2008-0.0862-0.03470.15630.00010.16416.63712.808212.0064
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 1:65 )A1 - 65
2X-RAY DIFFRACTION2( CHAIN A AND RESID 66:188 )A66 - 188
3X-RAY DIFFRACTION3( CHAIN B AND RESID 1:11 )B1 - 11
4X-RAY DIFFRACTION4( CHAIN B AND RESID 12:49 )B12 - 49
5X-RAY DIFFRACTION5( CHAIN B AND RESID 50:65 )B50 - 65
6X-RAY DIFFRACTION6( CHAIN B AND RESID 66:97 )B66 - 97
7X-RAY DIFFRACTION7( CHAIN B AND RESID 98:128 )B98 - 128
8X-RAY DIFFRACTION8( CHAIN B AND RESID 129:144 )B129 - 144
9X-RAY DIFFRACTION9( CHAIN B AND RESID 145:188 )B145 - 188

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