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- PDB-8aga: Structure of p-hydroxy benzoic acid ligand bound HosA transcripti... -

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Basic information

Entry
Database: PDB / ID: 8aga
TitleStructure of p-hydroxy benzoic acid ligand bound HosA transcriptional regulator from enteropathogenic Escherichia coli O127:H6 (strain E2348/69)
ComponentsTranscriptional regulator HosA
KeywordsDNA BINDING PROTEIN / Transcription factor / Flegella motility / Enteropathogenic E. coli / p-hydroxy benzoic acid sensor
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
P-HYDROXYBENZOIC ACID / Transcriptional regulator HosA
Similarity search - Component
Biological speciesEscherichia coli O127:H6 str. E2348/69 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.21 Å
AuthorsArpita, G. / Kannika, B.R. / Madan Kumar, S.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Structure of p-hydroxy benzoic acid ligand bound HosA transcriptional regulator from enteropathogenic Escherichia coli O127:H6 (strain E2348/69)
Authors: Arpita, G. / Kannika, B.R. / Madan Kumar, S.
History
DepositionJul 19, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 2, 2023Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Transcriptional regulator HosA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,8284
Polymers16,5921
Non-polymers2363
Water1,62190
1
A: Transcriptional regulator HosA
hetero molecules

A: Transcriptional regulator HosA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,6558
Polymers33,1842
Non-polymers4716
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555-x,y,-z1
Buried area6340 Å2
ΔGint-49 kcal/mol
Surface area13320 Å2
Unit cell
Length a, b, c (Å)67.380, 67.380, 95.040
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number95
Space group name H-MP4322
Space group name HallP4cw2c

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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
Source: (gene. exp.) Escherichia coli O127:H6 str. E2348/69 (bacteria)
Gene: hosA, E2348C_3010 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P69782
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-PHB / P-HYDROXYBENZOIC ACID


Mass: 138.121 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C7H6O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


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


Mass: 18.015 Da / Num. of mol.: 90 / 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: 3.48 Å3/Da / Density % sol: 64.6 %
Crystal growTemperature: 277.15 K / Method: microbatch
Details: Potassium Chloride, Calcium Chloride, Sodium Cacodylate, PEG4000, pH6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54179 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: May 20, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54179 Å / Relative weight: 1
ReflectionResolution: 2.21→54.97 Å / Num. obs: 11485 / % possible obs: 99.8 % / Redundancy: 7.3 % / Biso Wilson estimate: 21 Å2 / CC1/2: 0.998 / Net I/σ(I): 18.7
Reflection shellResolution: 2.21→2.33 Å / Redundancy: 6.8 % / Num. unique obs: 1612 / CC1/2: 0.946 / % possible all: 98.4

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487: ???refinement
PHENIX1.20.1_4487: ???refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7Z4P

7z4p
PDB Unreleased entry


Resolution: 2.21→47.64 Å / SU ML: 0.2287 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.8685
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.238 1146 10.01 %
Rwork0.2053 10302 -
obs0.2086 11448 99.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 22.92 Å2
Refinement stepCycle: LAST / Resolution: 2.21→47.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1045 0 15 91 1151
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00171084
X-RAY DIFFRACTIONf_angle_d0.47361456
X-RAY DIFFRACTIONf_chiral_restr0.0329159
X-RAY DIFFRACTIONf_plane_restr0.0037191
X-RAY DIFFRACTIONf_dihedral_angle_d4.1379146
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.21-2.310.25471380.22961236X-RAY DIFFRACTION98.14
2.31-2.440.26961380.21391257X-RAY DIFFRACTION100
2.44-2.590.24731420.2191267X-RAY DIFFRACTION100
2.59-2.790.26271400.23181262X-RAY DIFFRACTION100
2.79-3.070.26371440.2331292X-RAY DIFFRACTION100
3.07-3.510.24771420.20471274X-RAY DIFFRACTION100
3.51-4.420.19291450.17811309X-RAY DIFFRACTION100
4.43-47.640.23081570.19021405X-RAY DIFFRACTION99.68

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