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- PDB-8ssh: MtrR from Neisseria gonorrhoeae bound to Ethinyl Estradiol -

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Basic information

Entry
Database: PDB / ID: 8ssh
TitleMtrR from Neisseria gonorrhoeae bound to Ethinyl Estradiol
ComponentsHTH-type transcriptional regulator MtrR
KeywordsTRANSCRIPTION / HTH / regulator / hormone / induction
Function / homology
Function and homology information


Transcription regulator MAATS, C-terminal / MAATS-type transcriptional repressor, C-terminal region / : / DNA-binding HTH domain, TetR-type, conserved site / TetR-type HTH domain signature. / Tetracyclin repressor-like, C-terminal domain superfamily / Bacterial regulatory proteins, tetR family / DNA-binding HTH domain, TetR-type / TetR-type HTH domain profile. / Homeobox-like domain superfamily
Similarity search - Domain/homology
Ethinyl estradiol / PHOSPHATE ION / HTH-type transcriptional regulator MtrR
Similarity search - Component
Biological speciesNeisseria gonorrhoeae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsHooks, G.M. / Brennan, R.G.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: Nat Commun / Year: 2024
Title: Hormonal steroids induce multidrug resistance and stress response genes in Neisseria gonorrhoeae by binding to MtrR.
Authors: Hooks, G.M. / Ayala, J.C. / Holley, C.L. / Dhulipala, V. / Beggs, G.A. / Perfect, J.R. / Schumacher, M.A. / Shafer, W.M. / Brennan, R.G.
History
DepositionMay 8, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 14, 2024Provider: repository / Type: Initial release
Revision 1.1Apr 3, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: HTH-type transcriptional regulator MtrR
D: HTH-type transcriptional regulator MtrR
A: HTH-type transcriptional regulator MtrR
B: HTH-type transcriptional regulator MtrR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,76314
Polymers98,0084
Non-polymers1,75510
Water25214
1
C: HTH-type transcriptional regulator MtrR
D: HTH-type transcriptional regulator MtrR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,8827
Polymers49,0042
Non-polymers8785
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4140 Å2
ΔGint-48 kcal/mol
Surface area16460 Å2
MethodPISA
2
A: HTH-type transcriptional regulator MtrR
B: HTH-type transcriptional regulator MtrR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,8827
Polymers49,0042
Non-polymers8785
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3670 Å2
ΔGint-30 kcal/mol
Surface area16620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.923, 85.709, 211.556
Angle α, β, γ (deg.)90.000, 90.780, 90.000
Int Tables number5
Space group name H-MI121
Space group name HallC2y(x,y,-x+z)
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z+1/2
#4: -x+1/2,y+1/2,-z+1/2

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Components

#1: Protein
HTH-type transcriptional regulator MtrR / Multiple transferrable resistance regulator


Mass: 24501.990 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria gonorrhoeae (bacteria) / Gene: mtrR / Production host: Escherichia coli (E. coli) / References: UniProt: P39897
#2: Chemical
ChemComp-3WF / Ethinyl estradiol


Mass: 296.403 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C20H24O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 14 / 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: 2.68 Å3/Da / Density % sol: 54.08 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop
Details: 1200 mM Sodium phosphate monobasic/800 mM Potassium phosphate dibasic, 100 mM CAPS/Sodium hydroxide pH 10.5, 200 mM Lithium Sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 0.9765 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 24, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9765 Å / Relative weight: 1
ReflectionResolution: 3.2→43.52 Å / Num. obs: 16998 / % possible obs: 98.46 % / Redundancy: 1.9 % / CC1/2: 0.997 / Net I/σ(I): 11.53
Reflection shellResolution: 3.2→3.314 Å / Mean I/σ(I) obs: 2.3 / Num. unique obs: 1656 / CC1/2: 0.815

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 8FW0

8fw0


Resolution: 3.2→43.52 Å / SU ML: 0.482 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 33.6518
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2787 859 5.06 %
Rwork0.1995 16127 -
obs0.2036 16986 98.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 87.67 Å2
Refinement stepCycle: LAST / Resolution: 3.2→43.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5993 0 118 14 6125
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0096251
X-RAY DIFFRACTIONf_angle_d1.16728520
X-RAY DIFFRACTIONf_chiral_restr0.0549970
X-RAY DIFFRACTIONf_plane_restr0.00921065
X-RAY DIFFRACTIONf_dihedral_angle_d7.8169826
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2-3.40.37651420.28392637X-RAY DIFFRACTION97.68
3.4-3.660.35151430.24082687X-RAY DIFFRACTION99.12
3.66-4.030.28481400.20872678X-RAY DIFFRACTION98.88
4.03-4.610.31400.18272697X-RAY DIFFRACTION99.4
4.61-5.810.25671410.19132699X-RAY DIFFRACTION98
5.81-43.520.23911530.17942729X-RAY DIFFRACTION98.26
Refinement TLS params.Method: refined / Origin x: 2.4120131381 Å / Origin y: 30.0366632171 Å / Origin z: 23.9248958009 Å
111213212223313233
T0.52085927162 Å2-0.0537376519303 Å2-0.0745001481446 Å2-0.534017441542 Å20.0480560401864 Å2--0.508401412065 Å2
L0.617524391274 °2-0.557345900269 °2-0.15618106731 °2-2.0360780597 °20.660975303376 °2--0.942810527981 °2
S-0.056104752343 Å °-0.132114196329 Å °0.0549946597097 Å °0.0433811581952 Å °0.0475185199021 Å °-0.15725904305 Å °-0.0435370930258 Å °0.0529738732513 Å °-0.0212262676427 Å °
Refinement TLS groupSelection details: all

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