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- PDB-7ttv: E.coli DsbA in complex with 4-phenyl-2-(3-phenylpropyl)thiazole-5... -

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Basic information

Entry
Database: PDB / ID: 7ttv
TitleE.coli DsbA in complex with 4-phenyl-2-(3-phenylpropyl)thiazole-5-carboxylic acid
ComponentsThiol:disulfide interchange protein DsbA
KeywordsOXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR / Inhibitor / complex / disulfide oxidoreductase / fragments / 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
COPPER (II) ION / Chem-QVP / Thiol:disulfide interchange protein DsbA
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
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: Sci Rep / Year: 2022
Title: Methyl probes in proteins for determining ligand binding mode in weak protein-ligand complexes.
Authors: Mohanty, B. / Orts, J. / Wang, G. / Nebl, S. / Alwan, W.S. / Doak, B.C. / Williams, M.L. / Heras, B. / Mobli, M. / Scanlon, M.J.
History
DepositionFeb 2, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 12, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)42,6974
Polymers42,3102
Non-polymers3872
Water6,287349
1
A: Thiol:disulfide interchange protein DsbA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,4782
Polymers21,1551
Non-polymers3231
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)117.450, 63.740, 74.280
Angle α, β, γ (deg.)90.000, 125.870, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-424-

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 K-12 (bacteria) / Strain: K12 / Gene: dsbA, dsf, ppfA, b3860, JW3832 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0AEG4
#2: Chemical ChemComp-QVP / 4-phenyl-2-(3-phenylpropyl)-1,3-thiazole-5-carboxylic acid


Mass: 323.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H17NO2S / 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.: 349 / 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: 2.66 Å3/Da / Density % sol: 53.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: 11-13% PEG 8000, 5-7.5% glycerol, 1 mM copper(II) chloride, 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: Aug 3, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.986→60.193 Å / Num. all: 30753 / Num. obs: 30753 / % possible obs: 99.7 % / Redundancy: 4.1 % / Biso Wilson estimate: 23.88 Å2 / Rpim(I) all: 0.05 / Rrim(I) all: 0.101 / Rsym value: 0.088 / Net I/av σ(I): 7.9 / Net I/σ(I): 11.5 / Num. measured all: 125514
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique obsRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
1.99-2.0940.5561.41790544480.3160.6420.5562.499
2.09-2.224.10.3652.11735442160.2050.4190.3653.799.9
2.22-2.374.10.25731643039990.1450.2950.2575.299.9
2.37-2.564.10.19141527037090.1070.2190.1916.999.8
2.56-2.814.10.1226.21401034050.0680.140.12210.499.9
2.81-3.144.10.08391266930800.0470.0960.08314.399.8
3.14-3.634.10.05213.41129027460.0290.060.05221.699.8
3.63-4.444.10.03817.4944423260.0210.0430.03828.199.9
4.44-6.2840.03816.2728118050.0210.0430.03826.899.8
6.28-37.0793.80.03217386110190.0190.0370.03228.199.1

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
SCALA3.3.21data scaling
PDB_EXTRACT3.25data extraction
MOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1FVK

1fvk


Resolution: 1.99→37.08 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 23.91 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2271 1443 4.69 %
Rwork0.1806 29307 -
obs0.1828 30750 99.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 111.64 Å2 / Biso mean: 29.0546 Å2 / Biso min: 10.83 Å2
Refinement stepCycle: final / Resolution: 1.99→37.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2956 0 40 349 3345
Biso mean--68.56 34.42 -
Num. residues----376
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.99-2.060.31021260.26092914304099
2.06-2.140.31641590.232428823041100
2.14-2.240.2751330.219529433076100
2.24-2.350.27911570.206328813038100
2.35-2.50.26051450.200529433088100
2.5-2.70.25721260.194329233049100
2.7-2.970.2431250.192929623087100
2.97-3.40.241570.176229233080100
3.4-4.280.18731440.145229533097100
4.28-37.080.16931710.152129833154100

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