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- PDB-8fw3: MtrR from Neisseria gonorrhoeae bound to Testosterone -

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Basic information

Entry
Database: PDB / ID: 8fw3
TitleMtrR from Neisseria gonorrhoeae bound to Testosterone
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
PHOSPHATE ION / TESTOSTERONE / HTH-type transcriptional regulator MtrR
Similarity search - Component
Biological speciesNeisseria gonorrhoeae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.22 Å
AuthorsHooks, G.H. / 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
DepositionJan 20, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 24, 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
Revision 1.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)100,38713
Polymers98,7584
Non-polymers1,6299
Water1,20767
1
C: HTH-type transcriptional regulator MtrR
D: HTH-type transcriptional regulator MtrR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,2417
Polymers49,3792
Non-polymers8625
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5130 Å2
ΔGint-43 kcal/mol
Surface area16230 Å2
MethodPISA
2
A: HTH-type transcriptional regulator MtrR
B: HTH-type transcriptional regulator MtrR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,1466
Polymers49,3792
Non-polymers7674
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4990 Å2
ΔGint-43 kcal/mol
Surface area16040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.913, 84.868, 212.515
Angle α, β, γ (deg.)90.000, 92.251, 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: 24689.568 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-TES / TESTOSTERONE


Mass: 288.424 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C19H28O2 / Feature type: SUBJECT OF INVESTIGATION / Comment: hormone*YM
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 67 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.69 Å3/Da / Density % sol: 54.24 %
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: 5.0.2 / Wavelength: 0.97864 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Apr 30, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97864 Å / Relative weight: 1
ReflectionResolution: 2.22→48.37 Å / Num. obs: 51794 / % possible obs: 99.9 % / Redundancy: 7.3 % / Biso Wilson estimate: 52.59 Å2 / CC1/2: 0.999 / Net I/σ(I): 17.3
Reflection shellResolution: 2.22→2.29 Å / Num. unique obs: 4520 / CC1/2: 0.85 / % possible all: 99.9

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Processing

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

8fw0


Resolution: 2.22→48.37 Å / SU ML: 0.3076 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.3452
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2612 1453 2.81 %
Rwork0.2082 50287 -
obs0.2097 51740 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 62.11 Å2
Refinement stepCycle: LAST / Resolution: 2.22→48.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5979 0 109 67 6155
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086230
X-RAY DIFFRACTIONf_angle_d0.91648490
X-RAY DIFFRACTIONf_chiral_restr0.0493978
X-RAY DIFFRACTIONf_plane_restr0.00691053
X-RAY DIFFRACTIONf_dihedral_angle_d10.4821843
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.22-2.30.40421440.32995032X-RAY DIFFRACTION99.65
2.3-2.390.32941460.26734973X-RAY DIFFRACTION99.73
2.39-2.50.29411460.23874995X-RAY DIFFRACTION99.73
2.5-2.630.28921440.24335009X-RAY DIFFRACTION99.84
2.63-2.80.30151500.24165022X-RAY DIFFRACTION99.85
2.8-3.010.32411380.24935010X-RAY DIFFRACTION99.98
3.01-3.320.28011370.22995049X-RAY DIFFRACTION99.94
3.32-3.80.28611550.21455022X-RAY DIFFRACTION99.96
3.8-4.780.23891440.17075043X-RAY DIFFRACTION99.77
4.78-48.370.21511490.18995132X-RAY DIFFRACTION99.55
Refinement TLS params.Method: refined / Origin x: -31.3055719447 Å / Origin y: -15.1283573794 Å / Origin z: -23.8158220809 Å
111213212223313233
T0.460429127575 Å20.0433993702321 Å2-0.234018978212 Å2-0.360046406294 Å2-0.033695383331 Å2--0.571508861487 Å2
L0.475145399919 °20.308349517954 °2-0.0515857993166 °2-1.43985204588 °2-0.425272546897 °2--0.465122641258 °2
S-0.028489914294 Å °0.130581116283 Å °0.0531919725645 Å °0.0304371510116 Å °0.00885875460259 Å °0.0924775264993 Å °-0.0890427181015 Å °-0.000856709372209 Å °0.0149364501848 Å °
Refinement TLS groupSelection details: all

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