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- PDB-7ju3: MtrR bound to the mtrCDE operator from Neisseria gonorrhoeae -

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Basic information

Entry
Database: PDB / ID: 7ju3
TitleMtrR bound to the mtrCDE operator from Neisseria gonorrhoeae
Components
  • DNA (5'-D(*AP*CP*AP*TP*AP*CP*AP*CP*GP*AP*TP*TP*GP*CP*AP*CP*GP*GP*AP*TP*A)-3')
  • DNA (5'-D(*TP*AP*TP*CP*CP*GP*TP*GP*CP*AP*AP*TP*CP*GP*TP*GP*TP*AP*TP*GP*T)-3')
  • HTH-type transcriptional regulator MtrR
KeywordsDNA BINDING PROTEIN / TetR family / transcription / global 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: 2.7 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 19, 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
B: HTH-type transcriptional regulator MtrR
C: DNA (5'-D(*TP*AP*TP*CP*CP*GP*TP*GP*CP*AP*AP*TP*CP*GP*TP*GP*TP*AP*TP*GP*T)-3')
D: DNA (5'-D(*AP*CP*AP*TP*AP*CP*AP*CP*GP*AP*TP*TP*GP*CP*AP*CP*GP*GP*AP*TP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,0498
Polymers61,8884
Non-polymers1604
Water1,24369
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: assay for oligomerization
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8150 Å2
ΔGint-82 kcal/mol
Surface area22560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)153.273, 59.420, 69.508
Angle α, β, γ (deg.)90.000, 114.310, 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*AP*TP*CP*CP*GP*TP*GP*CP*AP*AP*TP*CP*GP*TP*GP*TP*AP*TP*GP*T)-3')


Mass: 6444.168 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(*AP*CP*AP*TP*AP*CP*AP*CP*GP*AP*TP*TP*GP*CP*AP*CP*GP*GP*AP*TP*A)-3')


Mass: 6440.201 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.: 4 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 69 / 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: 2.33 Å3/Da / Density % sol: 47.22 %
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: 8.3.1 / Wavelength: 1.116 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 22, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.116 Å / Relative weight: 1
ReflectionResolution: 2.7→69.842 Å / Num. obs: 15036 / % possible obs: 95.1 % / Redundancy: 2.7 % / Rmerge(I) obs: 0.071 / Rrim(I) all: 0.088 / Net I/σ(I): 7.7
Reflection shellResolution: 2.7→2.85 Å / Redundancy: 2 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 1809 / Rrim(I) all: 0.577 / % possible all: 79.4

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
PDB_EXTRACT3.25data extraction
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7JNP

7jnp


Resolution: 2.7→69.842 Å / SU ML: 0.39 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 35.53 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2823 1482 9.95 %
Rwork0.2276 13414 -
obs0.2329 14896 93.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 187.93 Å2 / Biso mean: 81.9299 Å2 / Biso min: 34.04 Å2
Refinement stepCycle: final / Resolution: 2.7→69.842 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3128 855 4 69 4056
Biso mean--107.4 78.67 -
Num. residues----447
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.7001-2.78730.42611070.364393774
2.7873-2.88690.36341240.3396112488
2.8869-3.00250.34861390.3048124296
3.0025-3.13910.3851390.2875128398
3.1391-3.30460.34021420.2985124898
3.3046-3.51170.34431330.2476126897
3.5117-3.78280.32811270.2878113989
3.7828-4.16340.30291400.2142128498
4.1634-4.76570.22791420.1764127698
4.7657-6.00380.24341430.2037129998
6.0038-69.8420.22341460.1815131498
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)
14.4919-1.9793-1.45891.81020.57431.22560.02480.1978-0.0947-0.42280.02780.532-0.1822-0.1084-0.02250.4908-0.0785-0.10840.38410.03430.7495-48.5104-8.9541-11.2778
23.45940.17850.58051.90230.3151.005-0.0985-0.362-0.5890.39370.25140.25360.1282-0.1222-0.18530.420.0376-0.00090.40950.11870.6773-49.0795-8.067611.8493
32.10170.57550.2593.0853.30933.55650.52620.09070.39330.20541.0869-1.4845-0.22760.7847-1.1320.60380.1025-0.07480.6699-0.17731.1195-12.7358-9.039-3.2263
42.7767-0.19510.21642.61972.16475.830.44470.49250.1435-0.24241.1826-1.23820.41361.1245-1.4230.64020.0168-0.01390.8019-0.24911.3247-12.443-8.9789-3.9652
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 'B' and resid 7 through 209)B7 - 209
3X-RAY DIFFRACTION3(chain 'C' and resid 1 through 21)C1 - 21
4X-RAY DIFFRACTION4(chain 'D' and resid 1 through 21)D1 - 21

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