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- PDB-8ycv: HosA transcriptional regulator from enteropathogenic Escherichia ... -

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Basic information

Entry
Database: PDB / ID: 8ycv
TitleHosA transcriptional regulator from enteropathogenic Escherichia coli O127:H6 (strain E2348/69) bound with 4-hydroxy benzoic acid - Conformation II at 2.16 angstrom resolution (STARANISO processed)
ComponentsTranscriptional regulator HosA
KeywordsDNA BINDING PROTEIN / Antibiotic resistance / MarR transcription factor / HosA / Enteropathogenic Escherichia coli / Paraben
Function / homology
Function and homology information


DNA-binding transcription factor activity / DNA binding
Similarity search - Function
Transcriptional regulator MarR-type, conserved site / MarR-type HTH domain signature. / MarR family / MarR-type HTH domain profile. / helix_turn_helix multiple antibiotic resistance protein / MarR-type HTH domain / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / P-HYDROXYBENZOIC ACID / Transcriptional regulator HosA
Similarity search - Component
Biological speciesEscherichia coli O127:H6 str. E2348/69 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.16 Å
AuthorsBrito, J.A. / Goswami, A.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: HosA transcriptional regulator from enteropathogenic Escherichia coli O127:H6 (strain E2348/69) bound with 4-hydroxy benzoic acid - Conformation II at 2.16 angstrom resolution (Staraniso processed)
Authors: Brito, J.A. / Goswami, A.
History
DepositionFeb 18, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 4, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Transcriptional regulator HosA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,9424
Polymers16,5921
Non-polymers3503
Water91951
1
A: Transcriptional regulator HosA
hetero molecules

A: Transcriptional regulator HosA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,8858
Polymers33,1842
Non-polymers7016
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation1
MethodPISA
Unit cell
Length a, b, c (Å)67.169, 67.169, 95.104
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number95
Space group name H-MP4322
Space group name HallP4cw2c
Symmetry operation#1: x,y,z
#2: -y,x,z+3/4
#3: y,-x,z+1/4
#4: x,-y,-z+1/2
#5: -x,y,-z
#6: -x,-y,z+1/2
#7: y,x,-z+1/4
#8: -y,-x,-z+3/4

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Components

#1: Protein Transcriptional regulator HosA


Mass: 16592.092 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: HosA protein
Source: (gene. exp.) Escherichia coli O127:H6 str. E2348/69 (bacteria)
Strain: E2348/69 / EPEC / Gene: hosA / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P69782
#2: Chemical ChemComp-PHB / P-HYDROXYBENZOIC ACID


Mass: 138.121 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H6O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 51 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 3.24 Å3/Da / Density % sol: 62.04 % / Description: Rod shaped
Crystal growTemperature: 277.15 K / Method: microbatch / pH: 6.2
Details: Sodium phosphate dibasic/ Potassium phosphate monobasic, Sodium chloride, PEG 200

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: RRCAT INDUS-2 / Beamline: PX-BL21 / Wavelength: 0.97893 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 13, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97893 Å / Relative weight: 1
ReflectionResolution: 2.16→67.17 Å / Num. obs: 8907 / % possible obs: 73.2 % / Redundancy: 6.8 % / Biso Wilson estimate: 30.44 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.135 / Rpim(I) all: 0.055 / Rrim(I) all: 0.147 / Net I/σ(I): 9.4
Reflection shellResolution: 2.16→2.33 Å / Redundancy: 4.1 % / Rmerge(I) obs: 1.022 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 445 / CC1/2: 0.46 / Rpim(I) all: 0.553 / Rrim(I) all: 1.172 / % possible all: 19.3

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Processing

Software
NameVersionClassification
autoPROC1.0.5 (20240123)data processing
XDSVERSION Jun 30, 2023 BUILT=20230630data reduction
Aimless0.7.15data scaling
STARANISO2.4.9 (20231025)data scaling
PHASER2.8.3phasing
Coot0.9.8.92model building
PHENIX1.21rc1_4903refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.16→67.17 Å / SU ML: 0.3176 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 26.8081
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2319 463 5.2 %
Rwork0.2018 8442 -
obs0.2035 8905 73.16 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 41.99 Å2
Refinement stepCycle: LAST / Resolution: 2.16→67.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1071 0 24 51 1146
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00271110
X-RAY DIFFRACTIONf_angle_d0.49951486
X-RAY DIFFRACTIONf_chiral_restr0.0332161
X-RAY DIFFRACTIONf_plane_restr0.0047194
X-RAY DIFFRACTIONf_dihedral_angle_d14.3608427
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.16-2.480.3218470.29111102X-RAY DIFFRACTION29.09
2.48-3.120.28881640.23813384X-RAY DIFFRACTION88.81
3.12-67.170.20912520.17993956X-RAY DIFFRACTION99.57
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)
11.68494535219-0.0639883218768-1.483771562182.326133172461.684149659845.7730828984-0.161264126130.1546754639-0.0558923964615-0.00535702950346-0.1646999087920.361758391472-0.24895721767-0.5914712225760.3299299450680.2928331737460.0492476390141-0.06185106181990.1787986649310.01538439516250.306249445316-38.7235517671-16.6211813521-3.84223666302
21.90336741659-0.661064963812-0.5870761886082.323611539280.8056958630224.79130806789-0.255526218094-0.1677503979360.07555995519720.02410247254690.133767259075-0.363814981673-0.2235901622551.283390786730.09408896287430.249839058689-0.0515220402678-0.02379399051420.4286372392880.06261742644620.244525789373-18.8214813227-21.3018471491-8.91951385747
32.24030766131-1.06604507215-0.7755381496385.095757987532.993835636653.37410700584-0.370729896191-0.139592949134-0.3356756467280.281089111188-0.2300678410320.4569741555260.6015515270550.3168097302160.2561884948270.3068149346680.1298280320030.1429779902440.324497036180.1610355421770.500653106824-21.6664395121-31.5805828936-7.15747058668
44.59072355954-0.6683946969830.4911818671451.619649088940.6256141584351.34600800108-0.190548988244-0.330356558494-0.2621080063650.1945319284-0.1120833556940.1905656665010.2847733421310.5588268246380.1661473156220.2896322937670.1408548892320.1198813862820.6889345631320.08224199213490.396794392222-15.7861979836-31.6423832594-14.8196412766
51.125771757410.484182795524-0.6851964158221.50227348931-0.8639729660970.667438487022-0.1515062894270.626033147933-0.425303488529-0.304897298903-0.153030619904-0.2983342396620.4457035065740.6386813964520.4025177102050.5042094089280.29840676110.1315290819611.133110318630.08605236255110.470423044074-4.67189416138-33.0842401512-4.47222043172
60.5196680121010.314410320307-0.309311512121.943958854850.9303751566732.87868176718-0.202066480895-0.0997867199658-0.206323014025-0.365037598203-0.009200604537750.157332891762-0.4630390079160.4482214477370.1634105250780.323750075531-0.0140058211271-0.02641583067160.2579450375770.07156070474140.203254760874-26.3965745276-18.571779454-16.7578793309
72.62880327215-0.4707922029110.4237448040550.682211535828-1.577878925933.841585627890.3745352147580.2014747832270.10855719891-0.352536498184-0.325351125238-0.488178348099-0.5728663209870.185646433092-0.06897642698820.5447538546730.01854085586390.05167572551330.145437963705-0.02332640239470.441062241776-28.9705291942-2.01758574794-2.21376867326
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 2 through 30 )2 - 301 - 29
22chain 'A' and (resid 31 through 58 )31 - 5830 - 57
33chain 'A' and (resid 59 through 71 )59 - 7158 - 70
44chain 'A' and (resid 72 through 79 )72 - 7971 - 78
55chain 'A' and (resid 80 through 86 )80 - 8679 - 85
66chain 'A' and (resid 87 through 116 )87 - 11686 - 115
77chain 'A' and (resid 117 through 134 )117 - 134116 - 133

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