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

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Basic information

Entry
Database: PDB / ID: 8xzu
TitleHosA transcriptional regulator from enteropathogenic Escherichia coli O127:H6 (strain E2348/69) bound with 4-hydroxy benzoic acid - Conformation II at 2.33 angstrom resolution
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: 2.33 Å
AuthorsManjunath, K. / Goswami, A.
Funding support India, 1items
OrganizationGrant numberCountry
Not funded India
CitationJournal: Biorxiv / Year: 2024
Title: Horizontally acquired HosA transcription factor bound with 4-hydroxy-benzoic acid exhibits unique tug-of-water dynamics.
Authors: Goswami, A. / Ullah, S. / Brito, J.A.
History
DepositionJan 21, 2024Deposition 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)16,8363
Polymers16,5921
Non-polymers2442
Water50428
1
A: Transcriptional regulator HosA
hetero molecules

A: Transcriptional regulator HosA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,6736
Polymers33,1842
Non-polymers4884
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation1
Unit cell
Length a, b, c (Å)67.290, 67.290, 95.270
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number95
Space group name H-MP4322

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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: obtained synthetically / Formula: C7H6O3
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 28 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 3.26 Å3/Da / Density % sol: 62.24 % / 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: 2.33→67.29 Å / Num. obs: 9878 / % possible obs: 100 % / Redundancy: 8.8 % / Biso Wilson estimate: 33.527 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.17 / Rpim(I) all: 0.06 / Rrim(I) all: 0.18 / Χ2: 0.92 / Net I/av σ(I): 10.5 / Net I/σ(I): 10.5
Reflection shellResolution: 2.33→2.41 Å / Redundancy: 8.5 % / Rmerge(I) obs: 1.524 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 933 / CC1/2: 0.543 / Rpim(I) all: 0.545 / Rrim(I) all: 1.621 / Χ2: 0.86

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Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158: ???)refinement
Aimless0.7.13data scaling
iMOSFLM7.4.0data reduction
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.33→67.29 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.15 / Stereochemistry target values: ML
Details: TLS refinement and pdb redo were used in intermediate steps of refinement. Last refinement was from Phenix.refine only.
RfactorNum. reflection% reflectionSelection details
Rfree0.2534 985 10 %Random selection
Rwork0.2342 ---
obs0.2364 9848 99.98 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 40.41 Å2
Refinement stepCycle: LAST / Resolution: 2.33→67.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1051 0 17 28 1096
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0011091
X-RAY DIFFRACTIONf_angle_d0.3971468
X-RAY DIFFRACTIONf_dihedral_angle_d4.716150
X-RAY DIFFRACTIONf_chiral_restr0.032162
X-RAY DIFFRACTIONf_plane_restr0.002192
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.33-2.460.36581360.32631222X-RAY DIFFRACTION100
2.46-2.610.33871360.29481229X-RAY DIFFRACTION100
2.61-2.810.28371390.28951247X-RAY DIFFRACTION100
2.81-3.090.29391380.2631246X-RAY DIFFRACTION100
3.09-3.540.28551420.22941270X-RAY DIFFRACTION100
3.54-4.460.22561410.2051278X-RAY DIFFRACTION100
4.47-67.290.20141530.20791371X-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)
12.6012-0.61041.87462.3691-1.38474.9331-0.3073-0.13270.37760.07970.0820.0058-0.1218-0.57820.22070.2643-0.01560.01590.2817-0.04550.2749-6.7369-11.2869-7.3324
21.0774-0.7206-0.78682.09510.42840.5792-0.4796-1.32821.05220.42650.592-0.0999-0.3099-0.7816-0.03270.44050.2148-0.19171.3374-0.24190.6071-25.0048-2.9889-9.2739
31.2787-1.09281.31813.1683-1.18443.18780.28660.2254-0.3437-0.6257-0.09690.18680.9970.1691-0.2150.4775-0.02670.03240.2539-0.01480.3902-3.5336-24.2622-10.5483
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 79 )
2X-RAY DIFFRACTION2chain 'A' and (resid 80 through 92 )
3X-RAY DIFFRACTION3chain 'A' and (resid 93 through 134 )

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