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- PDB-6of0: Structural basis for multidrug recognition and antimicrobial resi... -

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Basic information

Entry
Database: PDB / ID: 6of0
TitleStructural basis for multidrug recognition and antimicrobial resistance by MTRR, an efflux pump regulator from Neisseria Gonorrhoeae
ComponentsHTH-type transcriptional regulator MtrR
KeywordsDNA BINDING PROTEIN / TetR family / Helix-turn-helix (HTH) / transcription regulator
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. / Tetracycline Repressor, domain 2 / Tetracyclin repressor-like, C-terminal domain superfamily / Tetracycline Repressor; domain 2 / Bacterial regulatory proteins, tetR family / DNA-binding HTH domain, TetR-type ...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. / Tetracycline Repressor, domain 2 / Tetracyclin repressor-like, C-terminal domain superfamily / Tetracycline Repressor; domain 2 / Bacterial regulatory proteins, tetR family / DNA-binding HTH domain, TetR-type / TetR-type HTH domain profile. / Homeobox-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PHOSPHATE ION / HTH-type transcriptional regulator MtrR
Similarity search - Component
Biological speciesNeisseria gonorrhoeae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsBeggs, G.A. / Kumaraswami, M. / Shafer, W. / 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 Science Foundation (NSF, United States)DGE-1644868 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R37 AI021150-32 United States
CitationJournal: J.Bacteriol. / Year: 2019
Title: Structural, Biochemical, and In Vivo Characterization of MtrR-Mediated Resistance to Innate Antimicrobials by the Human Pathogen Neisseria gonorrhoeae .
Authors: Beggs, G.A. / Zalucki, Y.M. / Brown, N.G. / Rastegari, S. / Phillips, R.K. / Palzkill, T. / Shafer, W.M. / Kumaraswami, M. / Brennan, R.G.
History
DepositionMar 28, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 31, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 2, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.title ..._citation.journal_volume / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 7, 2020Group: Database references / Category: citation / Item: _citation.title
Revision 1.4Oct 11, 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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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)97,48910
Polymers96,9194
Non-polymers5706
Water4,360242
1
A: HTH-type transcriptional regulator MtrR
B: HTH-type transcriptional regulator MtrR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,8396
Polymers48,4592
Non-polymers3804
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3870 Å2
ΔGint-39 kcal/mol
Surface area16640 Å2
MethodPISA
2
C: HTH-type transcriptional regulator MtrR
D: HTH-type transcriptional regulator MtrR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,6494
Polymers48,4592
Non-polymers1902
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3950 Å2
ΔGint-36 kcal/mol
Surface area16770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)218.300, 84.600, 58.100
Angle α, β, γ (deg.)90.000, 103.900, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LYSLYSCYSCYS(chain 'A' and ((resid 10 through 13 and (name N...AA10 - 7210 - 72
12SERSERASNASN(chain 'A' and ((resid 10 through 13 and (name N...AA84 - 15084 - 150
13ASPASPARGARG(chain 'A' and ((resid 10 through 13 and (name N...AA152 - 208152 - 208
24LYSLYSCYSCYS(chain 'B' and ((resid 10 through 13 and (name N...BB10 - 7210 - 72
25SERSERASNASN(chain 'B' and ((resid 10 through 13 and (name N...BB84 - 15084 - 150
26ASPASPARGARG(chain 'B' and ((resid 10 through 13 and (name N...BB152 - 208152 - 208
37LYSLYSCYSCYS(chain 'C' and ((resid 10 through 13 and (name N...CC10 - 7210 - 72
38SERSERASNASN(chain 'C' and ((resid 10 through 13 and (name N...CC84 - 15084 - 150
39ASPASPARGARG(chain 'C' and ((resid 10 through 13 and (name N...CC152 - 208152 - 208
410LYSLYSCYSCYS(chain 'D' and ((resid 10 through 13 and (name N...DD10 - 7210 - 72
411SERSERASNASN(chain 'D' and ((resid 10 through 13 and (name N...DD84 - 15084 - 150
412ASPASPARGARG(chain 'D' and ((resid 10 through 13 and (name N...DD152 - 208152 - 208

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Components

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


Mass: 24229.732 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-PO4 / PHOSPHATE ION


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


Mass: 18.015 Da / Num. of mol.: 242 / 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: 2.87 Å3/Da / Density % sol: 57.15 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 1.7M NA/K PHOSPHATE, 0.18M LITHIUM SULFATE, 0.1M CAPS, PH 10.5

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Data collection

DiffractionMean temperature: 200 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 0.9797 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 20, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9797 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 65953 / % possible obs: 98.2 % / Redundancy: 2.17 % / Biso Wilson estimate: 42.74 Å2 / Rsym value: 0.097 / Net I/σ(I): 8.4
Reflection shellResolution: 2→2.02 Å / Num. unique obs: 1345 / Rsym value: 0.9

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
PHENIX1.15.2_3472refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3VIB

3vib


Resolution: 2→45.46 Å / SU ML: 0.3238 / Cross valid method: NONE / σ(F): 1.35 / Phase error: 28.9423
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2473 6676 10.13 %
Rwork0.2042 59236 -
obs0.2086 65912 94.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 55.46 Å2
Refinement stepCycle: LAST / Resolution: 2→45.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6009 0 30 242 6281
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00566168
X-RAY DIFFRACTIONf_angle_d0.748388
X-RAY DIFFRACTIONf_chiral_restr0.046965
X-RAY DIFFRACTIONf_plane_restr0.00541056
X-RAY DIFFRACTIONf_dihedral_angle_d12.76313556
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.020.41611570.40861345X-RAY DIFFRACTION65.13
2.02-2.050.39511640.38251427X-RAY DIFFRACTION69.75
2.05-2.070.36792220.36481824X-RAY DIFFRACTION88.69
2.07-2.10.40841800.33071870X-RAY DIFFRACTION88.74
2.1-2.120.32612260.30951873X-RAY DIFFRACTION91.74
2.12-2.150.35152220.30161994X-RAY DIFFRACTION94.78
2.15-2.180.34382430.2861999X-RAY DIFFRACTION97.9
2.18-2.220.33372310.29331995X-RAY DIFFRACTION97.63
2.22-2.250.36022260.31512025X-RAY DIFFRACTION97.36
2.25-2.290.35172310.2742041X-RAY DIFFRACTION97.93
2.29-2.330.2572240.22922054X-RAY DIFFRACTION98.32
2.33-2.370.2732030.22252035X-RAY DIFFRACTION98.55
2.37-2.420.27242390.21962052X-RAY DIFFRACTION98.41
2.42-2.470.24662220.22242030X-RAY DIFFRACTION98.25
2.47-2.520.27272250.22732054X-RAY DIFFRACTION98.53
2.52-2.580.29162320.22822040X-RAY DIFFRACTION98.57
2.58-2.640.27332400.2212070X-RAY DIFFRACTION98.76
2.64-2.710.26412190.20672033X-RAY DIFFRACTION98.82
2.71-2.790.26922200.20982063X-RAY DIFFRACTION98.66
2.79-2.880.25862300.21752057X-RAY DIFFRACTION98.83
2.88-2.990.23572280.21912036X-RAY DIFFRACTION98.48
2.99-3.110.28592150.21442080X-RAY DIFFRACTION98.79
3.11-3.250.28072510.21152044X-RAY DIFFRACTION98.46
3.25-3.420.272250.21122072X-RAY DIFFRACTION98.5
3.42-3.630.25242390.19252026X-RAY DIFFRACTION97.8
3.63-3.910.21252370.17072046X-RAY DIFFRACTION98.45
3.91-4.310.18692240.1572048X-RAY DIFFRACTION98.4
4.31-4.930.17472320.14312045X-RAY DIFFRACTION96.69
4.93-6.210.22782400.18712062X-RAY DIFFRACTION98.5
6.21-45.470.22642290.19941896X-RAY DIFFRACTION88.32
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)
12.08402165549-0.657551223713-0.8527001935051.503990076780.4520313350422.161897114610.04146902672430.1303397260190.1364100596370.029600325021-0.1900978186030.3094907800490.0917316691792-0.4686448026690.1341201510290.272487677448-0.01168323079330.01256266330160.370241303383-0.04910831458480.407619433197-42.171605262345.544819107410.9419030566
20.483178620276-0.1365157918320.388854298712.634092223391.319201046441.9288737485-0.02500112775170.03132028426560.1766563774070.1904885282810.0128392473824-0.2022011504230.01865760367630.2344198411150.01375182122930.286412809515-0.008752142388530.002809684221740.3050430808980.01943562491260.396703455729-21.561876804752.920018247819.7448111543
32.28119550977-0.7828658342780.3202985375422.33891206513-0.310686419131.706812733620.00899673414112-0.129879353002-0.103411125436-0.05033441447250.1231237146950.514821495757-0.125548238703-0.21329918931-0.1452498609780.3479749041740.0132472780276-0.0206158049940.3230742179740.05451324756060.3730982604854.0501597816511.306829870322.3395963528
41.904808509041.6656530133-0.3301527310182.11460289709-0.5966120431391.67652163259-0.0735761632753-0.033795435459-0.204758946656-0.07838787056930.117749332976-0.349790356399-0.09451044087320.214730072694-0.02877752430090.2879309819130.01222334686380.02098188914280.383072645281-0.07341162276450.27648363944927.171119405318.259990944122.7474395535
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and resid 8 through 209)
2X-RAY DIFFRACTION2(chain 'B' and resid 9 through 210)
3X-RAY DIFFRACTION3(chain 'C' and resid 9 through 209)
4X-RAY DIFFRACTION4(chain 'D' and resid 8 through 209)

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