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- PDB-7jnp: MtrR bound to the rpoH operator from Neisseria gonorrhoeae -

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Basic information

Entry
Database: PDB / ID: 7jnp
TitleMtrR bound to the rpoH operator from Neisseria gonorrhoeae
Components
  • DNA (5'-D(*TP*AP*CP*AP*TP*AP*CP*GP*TP*GP*GP*TP*TP*GP*TP*AP*TP*GP*TP*AP*A)-3')
  • DNA (5'-D(*TP*TP*AP*CP*AP*TP*AP*CP*AP*AP*CP*CP*AP*CP*GP*TP*AP*TP*GP*TP*A)-3')
  • HTH-type transcriptional regulator MtrR
KeywordsDNA BINDING PROTEIN / TetR family / transcription regulator / helix-turn-helix motif
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
DNA / DNA (> 10) / HTH-type transcriptional regulator MtrR
Similarity search - Component
Biological speciesNeisseria gonorrhoeae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsBeggs, G.A. / Shafer, W.M. / Brennan, R.G.
Funding support United States, 4items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R05 AI048593-09 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)1R01AI109096-01A1 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R37 AI021150-32 United States
National Science Foundation (NSF, United States)DGE-1644868 United States
CitationJournal: Nucleic Acids Res. / Year: 2021
Title: Structures of Neisseria gonorrhoeae MtrR-operator complexes reveal molecular mechanisms of DNA recognition and antibiotic resistance-conferring clinical mutations.
Authors: Beggs, G.A. / Ayala, J.C. / Kavanaugh, L.G. / Read, T.D. / Hooks, G.M. / Schumacher, M.A. / Shafer, W.M. / Brennan, R.G.
History
DepositionAug 5, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 24, 2021Provider: repository / Type: Initial release
Revision 1.1Apr 21, 2021Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Apr 28, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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
C: DNA (5'-D(*TP*TP*AP*CP*AP*TP*AP*CP*AP*AP*CP*CP*AP*CP*GP*TP*AP*TP*GP*TP*A)-3')
D: DNA (5'-D(*TP*AP*CP*AP*TP*AP*CP*GP*TP*GP*GP*TP*TP*GP*TP*AP*TP*GP*TP*AP*A)-3')
B: HTH-type transcriptional regulator MtrR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,20712
Polymers61,8864
Non-polymers3218
Water1,22568
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: assay for oligomerization
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8490 Å2
ΔGint-111 kcal/mol
Surface area21740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)150.990, 58.125, 68.205
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 24501.990 Da / Num. of mol.: 2
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: DNA chain DNA (5'-D(*TP*TP*AP*CP*AP*TP*AP*CP*AP*AP*CP*CP*AP*CP*GP*TP*AP*TP*GP*TP*A)-3')


Mass: 6390.175 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria gonorrhoeae (bacteria) / Production host: Escherichia coli (E. coli)
#3: DNA chain DNA (5'-D(*TP*AP*CP*AP*TP*AP*CP*GP*TP*GP*GP*TP*TP*GP*TP*AP*TP*GP*TP*AP*A)-3')


Mass: 6492.219 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria gonorrhoeae (bacteria) / Production host: Escherichia coli (E. coli)
#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 68 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.44 Å3/Da / Density % sol: 49.58 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 200 mM calcium acetate, 100 mM Tris-HCl pH 7.5, 27% Polyethylene glycol MW-8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 27, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.6→50.61 Å / Num. obs: 18276 / % possible obs: 99.3 % / Redundancy: 3.3 % / CC1/2: 0.992 / Rmerge(I) obs: 0.071 / Rpim(I) all: 0.045 / Rrim(I) all: 0.085 / Net I/σ(I): 6.9 / Num. measured all: 60808 / Scaling rejects: 24
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.6-2.723.40.34740821970.920.2180.4063.398
9.01-50.613.10.0414684700.9780.0280.04910.198.4

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Processing

Software
NameVersionClassification
Aimless0.7.3data scaling
PHENIX1.15.2_3472refinement
PDB_EXTRACT3.25data extraction
iMOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6OF0

6of0


Resolution: 2.6→50.608 Å / SU ML: 0.4 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 29.05 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2563 1831 10.03 %
Rwork0.1985 16418 -
obs0.2042 18249 99.06 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 131.31 Å2 / Biso mean: 52.2757 Å2 / Biso min: 11.42 Å2
Refinement stepCycle: final / Resolution: 2.6→50.608 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3124 855 8 68 4055
Biso mean--84.69 44.59 -
Num. residues----445
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.6004-2.67070.36241330.2744120897
2.6707-2.74930.3041440.25721272100
2.7493-2.8380.34711390.24911261100
2.838-2.93950.30461380.2371124399
2.9395-3.05710.29091410.24661263100
3.0571-3.19620.39311400.245126399
3.1962-3.36470.26561410.2032125299
3.3647-3.57550.25181390.193125399
3.5755-3.85150.25471430.1785127699
3.8515-4.23890.20461400.1661281100
4.2389-4.85180.19671450.1538126399
4.8518-6.11110.20431420.19321276100
6.1111-50.6080.27271460.1963130798
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)
13.2543-1.0711-0.55531.3340.46530.60870.04010.34650.0438-0.2492-0.10910.152-0.0983-0.02750.04560.3603-0.0087-0.01510.33020.0820.3549-48.1715-6.4903-11.3221
22.2822-0.84190.75611.651.51376.49160.4138-0.0196-0.0880.14720.5941-0.3070.41580.8214-0.77190.37840.0153-0.0270.5922-0.01490.4791-12.4401-6.25481.426
32.02110.873-0.40211.49861.43287.37620.39570.1992-0.0595-0.07880.4728-0.2179-0.27760.6332-0.71580.34560.00460.03580.64670.00790.4686-12.4392-6.34661.8232
43.58581.05360.75491.2880.51480.615-0.0067-0.3831-0.04020.1984-0.04020.15730.0911-0.04980.03130.35670.0170.02280.31370.07230.3545-48.2182-6.299511.3024
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain 'A' and resid 8 through 209)A8 - 209
2X-RAY DIFFRACTION2(chain 'C' and resid 1 through 21)C1 - 21
3X-RAY DIFFRACTION3(chain 'D' and resid 1 through 21)D1 - 21
4X-RAY DIFFRACTION4(chain 'B' and resid 9 through 209)B9 - 209

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