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- PDB-8xb7: HosA transcriptional regulator from enteropathogenic Escherichia ... -

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Basic information

Entry
Database: PDB / ID: 8xb7
TitleHosA transcriptional regulator from enteropathogenic Escherichia coli O127:H6 (strain E2348/69) bound with 4-hydroxy benzoic acid - Conformation II at 2.6 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
P-HYDROXYBENZOIC ACID / Transcriptional regulator HosA
Similarity search - Component
Biological speciesEscherichia coli O127:H6 str. E2348/69 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsGoswami, A. / Raju, R. / Kasarla, M.
Funding support India, 1items
OrganizationGrant numberCountry
Not funded India
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
DepositionDec 6, 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

Downloads & links

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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
Water23413
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 area5300 Å2
ΔGint-33 kcal/mol
Surface area13690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.640, 66.640, 94.490
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 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 13 / 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: 3.17 Å3/Da / Density % sol: 61.19 %
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: Sep 12, 2023 / Details: Tube
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54187 Å / Relative weight: 1
ReflectionResolution: 2.6→66.64 Å / Num. obs: 6948 / % possible obs: 99.6 % / Redundancy: 6.1 % / Biso Wilson estimate: 35.5317 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.084 / Rpim(I) all: 0.036 / Rrim(I) all: 0.092 / Net I/σ(I): 16.1
Reflection shellResolution: 2.6→2.74 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.435 / Mean I/σ(I) obs: 4.4 / Num. unique obs: 966 / CC1/2: 0.839 / Rpim(I) all: 0.188 / Rrim(I) all: 0.475 / % possible all: 99

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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: 2.6→54.46 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 22.42 / Stereochemistry target values: ML / Details: TLS refinement was on in all refinement steps.
RfactorNum. reflection% reflectionSelection details
Rfree0.2487 692 9.98 %Random selection
Rwork0.203 ---
obs0.2075 6935 99.38 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 40.92 Å2
Refinement stepCycle: LAST / Resolution: 2.6→54.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1058 0 10 13 1081
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0021094
X-RAY DIFFRACTIONf_angle_d0.5281470
X-RAY DIFFRACTIONf_dihedral_angle_d4.211147
X-RAY DIFFRACTIONf_chiral_restr0.034159
X-RAY DIFFRACTIONf_plane_restr0.004194
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.80.31861330.25381201X-RAY DIFFRACTION99
2.8-3.090.29241350.24231207X-RAY DIFFRACTION99
3.09-3.530.25331380.21151238X-RAY DIFFRACTION99
3.53-4.450.22381390.17671258X-RAY DIFFRACTION100
4.45-54.460.23131470.19221339X-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)
11.29940.29-1.67760.55091.11186.62650.06880.22940.0913-0.0612-0.11220.03550.1419-0.77290.07390.33340.0096-0.03190.25710.01730.3191-6.04517.7905-2.1721
23.6404-1.22940.25031.4653-0.19032.6389-0.13250.0373-0.1277-0.2032-0.0152-0.2110.01870.23120.19630.35-0.01870.01790.19980.02010.293612.670811.1868-11.1668
35.6255-2.00281.07886.32611.51329.3098-0.8782-0.8295-0.165-0.3606-0.08670.4242-0.5883-0.27440.83420.35540.0464-0.06390.4190.16730.591212.10594.6314-6.0941
47.40430.4861.69314.3382-0.47125.48620.52030.2786-1.4322-0.66080.00080.38760.36490.1415-0.12950.46040.1493-0.00740.41-0.07040.534517.96961.6561-14.9857
53.47972.2229-2.2511.4738-0.95755.7171-1.0883-0.34580.35391.11621.23081.13440.1074-0.6337-0.12950.57690.16930.28861.14040.0650.808329.07720.6291-4.1655
63.0648-0.2758-0.71581.3653-0.30653.1853-0.0810.1082-0.1574-0.3495-0.05610.081-0.15440.25350.1350.2833-0.1014-0.02740.26470.07490.22217.20314.7223-16.7087
72.5885-1.02890.20024.6813-1.12525.28220.22270.18180.4955-0.4573-0.456-0.6139-0.22170.62460.23010.3905-0.04360.04060.2343-0.02380.48824.58131.0468-2.3708
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 25 )
2X-RAY DIFFRACTION2chain 'A' and (resid 26 through 52 )
3X-RAY DIFFRACTION3chain 'A' and (resid 53 through 71 )
4X-RAY DIFFRACTION4chain 'A' and (resid 72 through 79 )
5X-RAY DIFFRACTION5chain 'A' and (resid 80 through 86 )
6X-RAY DIFFRACTION6chain 'A' and (resid 87 through 116 )
7X-RAY DIFFRACTION7chain 'A' and (resid 117 through 134 )

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