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- PDB-8wsv: Pre-binding structure of HosA transcriptional regulator from ente... -

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Basic information

Entry
Database: PDB / ID: 8wsv
TitlePre-binding structure of HosA transcriptional regulator from enteropathogenic Escherichia coli O127:H6 (strain E2348/69) in presence of sub optimal concentration of 4-hydroxy benzoic acid
ComponentsTranscriptional regulator HosA
KeywordsDNA BINDING PROTEIN / Antibiotic resistance / MarR transcription factor / HosA / Enteropathogenic Escherichia coli
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: 2.01 Å
AuthorsGoswami, A. / Raju, R. / Kasarla, M. / Ullah, S.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Biorxiv / Year: 2024
Title: Pre-binding structure of HosA transcriptional regulator from enteropathogenic Escherichia coli O127:H6 (strain E2348/69) in presence of sub optimal concentration of 4-hydroxy benzoic acid
Authors: Arpita, G. / Rukmini, R. / Mallesham, K. / Samee, U.
History
DepositionOct 17, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 28, 2024Provider: repository / Type: Initial release

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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)16,7302
Polymers16,5921
Non-polymers1381
Water2,486138
1
A: Transcriptional regulator HosA
hetero molecules

A: Transcriptional regulator HosA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,4604
Polymers33,1842
Non-polymers2762
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555-x,y,-z1
Buried area5450 Å2
ΔGint-33 kcal/mol
Surface area13240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.470, 67.470, 95.220
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number95
Space group name H-MP4322
Components on special symmetry positions
IDModelComponents
11A-394-

HOH

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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)
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: isolated from a natural source / Formula: C7H6O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 138 / 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: 3.52 Å3/Da / Density % sol: 65.06 %
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: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.54187 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Aug 8, 2023 / Details: Tube
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54187 Å / Relative weight: 1
ReflectionResolution: 2.01→67.47 Å / Num. obs: 14952 / % possible obs: 98.1 % / Redundancy: 7 % / Biso Wilson estimate: 13.28 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.065 / Rpim(I) all: 0.026 / Rrim(I) all: 0.07 / Net I/σ(I): 21
Reflection shellResolution: 2.01→2.12 Å / Redundancy: 7 % / Rmerge(I) obs: 0.116 / Mean I/σ(I) obs: 13 / Num. unique obs: 2096 / CC1/2: 0.992 / Rpim(I) all: 0.046 / Rrim(I) all: 0.125 / % possible all: 96.6

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Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158: ???)refinement
SCALA3.3.22data scaling
iMOSFLM7.4.0data reduction
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 8PQ4

8pq4


Resolution: 2.01→42.65 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.85 / Stereochemistry target values: ML
Details: TLS refinement along with occupancy was carried out for few steps. Once the partial density of the ligand was clear which aligned perfectly with ligand present in 8AGA, PHB was modeled with ...Details: TLS refinement along with occupancy was carried out for few steps. Once the partial density of the ligand was clear which aligned perfectly with ligand present in 8AGA, PHB was modeled with partial occupancy and the structure was refined using 8AGA as reference model and TLS = off.
RfactorNum. reflection% reflectionSelection details
Rfree0.2514 1495 10.02 %Random selection
Rwork0.23 ---
obs0.2322 14925 97.41 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 16.45 Å2
Refinement stepCycle: LAST / Resolution: 2.01→42.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1041 0 10 138 1189
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0021075
X-RAY DIFFRACTIONf_angle_d0.4321447
X-RAY DIFFRACTIONf_dihedral_angle_d4.172144
X-RAY DIFFRACTIONf_chiral_restr0.03158
X-RAY DIFFRACTIONf_plane_restr0.003190
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.01-2.070.28761300.24211176X-RAY DIFFRACTION96
2.07-2.150.28721310.24321169X-RAY DIFFRACTION97
2.15-2.230.29331310.24091180X-RAY DIFFRACTION96
2.23-2.330.2611320.23911187X-RAY DIFFRACTION96
2.33-2.460.28981330.23131197X-RAY DIFFRACTION97
2.46-2.610.25991330.25281196X-RAY DIFFRACTION98
2.61-2.810.27911370.25551235X-RAY DIFFRACTION98
2.81-3.090.25631360.25371217X-RAY DIFFRACTION98
3.09-3.540.22211390.23171253X-RAY DIFFRACTION98
3.54-4.460.21551410.19711261X-RAY DIFFRACTION98
4.46-42.650.23551520.20921359X-RAY DIFFRACTION99

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