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- PDB-8fw8: MtrR from Neisseria gonorrhoeae bound to Progesterone -

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Basic information

Entry
Database: PDB / ID: 8fw8
TitleMtrR from Neisseria gonorrhoeae bound to Progesterone
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 / PROGESTERONE / HTH-type transcriptional regulator MtrR
Similarity search - Component
Biological speciesNeisseria gonorrhoeae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.31 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)99,64813
Polymers98,0084
Non-polymers1,6409
Water91951
1
A: HTH-type transcriptional regulator MtrR
B: HTH-type transcriptional regulator MtrR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,7306
Polymers49,0042
Non-polymers7264
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5360 Å2
ΔGint-22 kcal/mol
Surface area16050 Å2
MethodPISA
2
C: HTH-type transcriptional regulator MtrR
D: HTH-type transcriptional regulator MtrR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,9187
Polymers49,0042
Non-polymers9145
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5460 Å2
ΔGint-31 kcal/mol
Surface area16080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.180, 85.048, 211.805
Angle α, β, γ (deg.)90.00, 91.24, 90.00
Int Tables number5
Space group name H-MI121
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-CXS / 3-CYCLOHEXYL-1-PROPYLSULFONIC ACID


Mass: 221.317 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H19NO3S / Comment: pH buffer*YM
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-STR / PROGESTERONE


Mass: 314.462 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C21H30O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 51 / 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: 2.65 Å3/Da / Density % sol: 53.63 %
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: 5.0.1 / Wavelength: 0.97741 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jun 25, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97741 Å / Relative weight: 1
ReflectionResolution: 2.31→48.01 Å / Num. obs: 44481 / % possible obs: 98.1 % / Redundancy: 3.3 % / Biso Wilson estimate: 55.62 Å2 / CC1/2: 0.999 / Net I/σ(I): 14.6
Reflection shellResolution: 2.31→2.4 Å / Num. unique obs: 4510 / CC1/2: 0.886

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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: 2.31→48.01 Å / SU ML: 0.308 / Cross valid method: FREE R-VALUE / Phase error: 29.266
Stereochemistry target values: GEOSTD + MONOMER LIBRARY + CDL V1.2
RfactorNum. reflection% reflection
Rfree0.251 --
Rwork0.21 --
obs-44455 98.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 66.12 Å2
Refinement stepCycle: LAST / Resolution: 2.31→48.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5955 0 108 51 6114
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086203
X-RAY DIFFRACTIONf_angle_d0.8288443
X-RAY DIFFRACTIONf_dihedral_angle_d13.978847
X-RAY DIFFRACTIONf_chiral_restr0.312956
X-RAY DIFFRACTIONf_plane_restr0.0061061
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.31-2.40.32061450.26674858X-RAY DIFFRACTION100
2.4-2.510.27081520.24874869X-RAY DIFFRACTION100
2.51-2.640.30741470.2564863X-RAY DIFFRACTION100
2.64-2.810.29611500.26734845X-RAY DIFFRACTION100
2.81-3.030.30361460.25324878X-RAY DIFFRACTION99
3.03-3.330.25381480.2414734X-RAY DIFFRACTION98
3.33-3.810.28341480.21584664X-RAY DIFFRACTION95
3.81-4.80.20981420.17774609X-RAY DIFFRACTION94
4.8-48.010.22931480.18794809X-RAY DIFFRACTION96
Refinement TLS params.Method: refined / Origin x: -2.2965 Å / Origin y: -17.0617 Å / Origin z: -23.529 Å
111213212223313233
T0.3893 Å20.0677 Å2-0.067 Å2-0.4279 Å2-0.0264 Å2--0.3838 Å2
L0.5051 °20.5742 °2-0.1473 °2-1.7957 °2-0.5067 °2--0.5793 °2
S-0.0355 Å °0.1044 Å °0.0694 Å °-0.0109 Å °0.0173 Å °0.1273 Å °-0.0877 Å °-0.0525 Å °0.0161 Å °
Refinement TLS groupSelection details: ALL

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