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- PDB-8pq4: Structure of HosA transcriptional regulator from enteropathogenic... -

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Basic information

Entry
Database: PDB / ID: 8pq4
TitleStructure of HosA transcriptional regulator from enteropathogenic Escherichia coli O127:H6 (strain E2348/69)
ComponentsTranscriptional regulator HosA
KeywordsDNA BINDING PROTEIN / HosA / Transcription factor / Flagellar motility / Enteropathogenic E. 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-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily ...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-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Transcriptional regulator HosA
Similarity search - Component
Biological speciesEscherichia coli O127:H6 str. E2348/69 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsArpita, G. / Kavyashree, M. / Kannika, B.R. / Madan Kumar, S.
Funding support India, 1items
OrganizationGrant numberCountry
Not funded India
CitationJournal: Biorxiv / Year: 2024
Title: Crystal structure of a MarR family transcriptional regulator protein
Authors: Goswami, A. / Ravindranath, K.B. / Shankar, M.K.
History
DepositionJul 10, 2023Deposition site: PDBE / Processing site: PDBE
SupersessionJul 19, 2023ID: 7Z4P, 7ZP4
Revision 1.0Jul 19, 2023Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.2Jan 29, 2025Group: Advisory / Database references / Structure summary
Category: citation / citation_author ...citation / citation_author / pdbx_database_PDB_obs_spr / pdbx_database_related / pdbx_entry_details
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _pdbx_database_PDB_obs_spr.replace_pdb_id / _pdbx_entry_details.has_protein_modification

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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)16,6542
Polymers16,5921
Non-polymers621
Water1,802100
1
A: Transcriptional regulator HosA
hetero molecules

A: Transcriptional regulator HosA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,3084
Polymers33,1842
Non-polymers1242
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_556-x,y,-z+11
Buried area4730 Å2
ΔGint-33 kcal/mol
Surface area13830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.160, 67.160, 95.660
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
Source: (gene. exp.) Escherichia coli O127:H6 str. E2348/69 (bacteria)
Strain: E2348/69 / EPEC / Gene: hosA, E2348C_3010 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P69782
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 100 / 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: 3.48 Å3/Da / Density % sol: 64.67 % / Description: Rod shaped
Crystal growTemperature: 277.15 K / Method: microbatch / pH: 5.6 / Details: Ammonium acetate, Bis Tris HCl, PEG 3350

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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: Dec 1, 2021 / Details: Mirrors
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: 11402 / % possible obs: 99 % / Redundancy: 6.7 % / Biso Wilson estimate: 15.204 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.14 / Rpim(I) all: 0.058 / Rrim(I) all: 0.152 / Net I/σ(I): 9.3
Reflection shellResolution: 2.21→2.33 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.76 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 1524 / CC1/2: 0.669 / Rpim(I) all: 0.321 / Rrim(I) all: 0.827 / % possible all: 93.3

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Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158)refinement
MAR345data collection
iMOSFLM7.4.0data reduction
SCALA3.3.22data scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.25→47.49 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.47 / Stereochemistry target values: ML
Details: The structure was refined with experimental mtz (from scala) and 10% Rfree test sets for initial few steps of refinement. Later several steps and final refinement were done with 5% test set.
RfactorNum. reflection% reflectionSelection details
Rfree0.258 546 5 %Random selection
Rwork0.2122 ---
obs0.2144 10925 99.95 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 31.05 Å2
Refinement stepCycle: LAST / Resolution: 2.25→47.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1023 0 4 101 1128
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0021043
X-RAY DIFFRACTIONf_angle_d0.4821404
X-RAY DIFFRACTIONf_dihedral_angle_d4.059140
X-RAY DIFFRACTIONf_chiral_restr0.032157
X-RAY DIFFRACTIONf_plane_restr0.003183
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.25-2.480.32351300.24772529X-RAY DIFFRACTION100
2.48-2.830.29181170.24922556X-RAY DIFFRACTION100
2.84-3.570.26181450.21812573X-RAY DIFFRACTION100
3.57-47.490.22931540.1872721X-RAY DIFFRACTION100

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