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- PDB-6nsn: TetR family transcriptional regulator CifR C99T-C181R Cysteines m... -

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Basic information

Entry
Database: PDB / ID: 6nsn
TitleTetR family transcriptional regulator CifR C99T-C181R Cysteines mutant complexed with 26bp double-strand operator DNA
Components
  • (DNA (26-MER)) x 2
  • (TetR family transcriptional regulator ...) x 2
KeywordsTRANSCRIPTION/DNA / Repressor / DNA-binding complex / Epoxide sensing / TRANSCRIPTION-DNA complex
Function / homology
Function and homology information


regulation of biosynthetic process / regulation of primary metabolic process / DNA-binding transcription repressor activity / protein-DNA complex / transcription cis-regulatory region binding / negative regulation of DNA-templated transcription / DNA binding
Similarity search - Function
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) / Putative transcriptional regulator / CifR
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsHe, S. / Simard, A.R. / Madden, D.R.
Funding support United States, 4items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01-AI091699 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P20-GM113132 United States
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)P30-DK117469 United States
Cystic Fibrosis FoundationSTANTO19R0 United States
CitationJournal: Biorxiv / Year: 2024
Title: Molecular basis for the transcriptional regulation of an epoxide-based virulence circuit in Pseudomonas aeruginosa
Authors: He, S. / Taher, N.M. / Simard, A.R. / Hvorecny, K.L. / Ragusa, M.J. / Bahl, C.D. / Hickman, A.B. / Dyda, F. / Madden, D.R.
History
DepositionJan 25, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 29, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Jan 31, 2024Group: Database references / Source and taxonomy / Structure summary
Category: citation / citation_author ...citation / citation_author / entity / entity_name_com / entity_src_gen / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _entity.pdbx_description / _entity_src_gen.pdbx_gene_src_gene / _struct_ref.db_code / _struct_ref.pdbx_db_accession / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq_dif.pdbx_seq_db_accession_code
Revision 1.3Feb 14, 2024Group: Source and taxonomy / Structure summary / Category: entity / entity_src_gen
Item: _entity.pdbx_description / _entity_src_gen.gene_src_strain ..._entity.pdbx_description / _entity_src_gen.gene_src_strain / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name
Revision 2.0Jul 17, 2024Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Data collection / Database references / Derived calculations / Non-polymer description / Other / Polymer sequence / Refinement description / Source and taxonomy / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / audit_author / cell / chem_comp / chem_comp_atom / chem_comp_bond / citation_author / entity / entity_poly / entity_poly_seq / entity_src_gen / ndb_struct_na_base_pair / ndb_struct_na_base_pair_step / pdbx_audit_support / pdbx_contact_author / pdbx_database_related / pdbx_entity_nonpoly / pdbx_entity_src_syn / pdbx_entry_details / pdbx_initial_refinement_model / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_refine_tls / pdbx_refine_tls_group / pdbx_related_exp_data_set / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_mod_residue / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_rmsd_angle / pdbx_validate_rmsd_bond / pdbx_validate_torsion / refine / refine_hist / refine_ls_restr / refine_ls_shell / reflns / reflns_shell / software / struct_asym / struct_conf / struct_conn / struct_conn_type / struct_ref / struct_ref_seq / symmetry
Item: _cell.Z_PDB / _cell.volume ..._cell.Z_PDB / _cell.volume / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _ndb_struct_na_base_pair.buckle / _ndb_struct_na_base_pair.hbond_type_28 / _ndb_struct_na_base_pair.opening / _ndb_struct_na_base_pair.propeller / _ndb_struct_na_base_pair.shear / _ndb_struct_na_base_pair.stagger / _ndb_struct_na_base_pair.stretch / _ndb_struct_na_base_pair_step.helical_rise / _ndb_struct_na_base_pair_step.helical_twist / _ndb_struct_na_base_pair_step.inclination / _ndb_struct_na_base_pair_step.rise / _ndb_struct_na_base_pair_step.roll / _ndb_struct_na_base_pair_step.shift / _ndb_struct_na_base_pair_step.slide / _ndb_struct_na_base_pair_step.tilt / _ndb_struct_na_base_pair_step.tip / _ndb_struct_na_base_pair_step.twist / _ndb_struct_na_base_pair_step.x_displacement / _ndb_struct_na_base_pair_step.y_displacement / _pdbx_contact_author.id / _pdbx_entity_src_syn.entity_id / _pdbx_initial_refinement_model.details / _pdbx_poly_seq_scheme.auth_mon_id / _pdbx_poly_seq_scheme.entity_id / _pdbx_poly_seq_scheme.mon_id / _pdbx_poly_seq_scheme.pdb_mon_id / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.value / _refine.B_iso_mean / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work / _refine.ls_R_factor_obs / _refine.ls_d_res_low / _refine.ls_number_reflns_R_work / _refine.overall_SU_ML / _refine.pdbx_overall_phase_error / _refine.pdbx_solvent_vdw_probe_radii / _refine.pdbx_stereochemistry_target_values / _refine.solvent_model_details / _refine_hist.d_res_low / _refine_hist.number_atoms_solvent / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_ligand / _refine_hist.pdbx_number_atoms_protein / _refine_ls_restr.dev_ideal / _refine_ls_restr.number / _refine_ls_restr.type / _refine_ls_shell.R_factor_R_free / _refine_ls_shell.R_factor_R_work / _refine_ls_shell.d_res_high / _refine_ls_shell.d_res_low / _refine_ls_shell.number_reflns_R_work / _refine_ls_shell.percent_reflns_obs / _reflns.B_iso_Wilson_estimate / _reflns.d_resolution_low / _reflns.number_obs / _reflns.pdbx_CC_star / _reflns.pdbx_Rmerge_I_obs / _reflns.pdbx_Rpim_I_all / _reflns.pdbx_Rrim_I_all / _reflns.pdbx_netI_over_sigmaI / _reflns.percent_possible_obs / _reflns_shell.Rmerge_I_obs / _reflns_shell.number_unique_obs / _reflns_shell.pdbx_CC_star / _reflns_shell.pdbx_Rpim_I_all / _reflns_shell.pdbx_Rrim_I_all / _reflns_shell.pdbx_redundancy / _reflns_shell.percent_possible_all / _struct_conf.beg_auth_comp_id / _struct_conf.beg_label_comp_id / _struct_conf.end_auth_comp_id / _struct_conf.end_auth_seq_id / _struct_conf.end_label_comp_id / _struct_conf.end_label_seq_id / _struct_conf.pdbx_PDB_helix_length / _struct_ref_seq.ref_id / _symmetry.space_group_name_Hall
Description: Real space R-factor
Details: Incorporated TLS and nucleic acid secondary structure restraints into refinement and made manual corrections to improve overall model geometry and clash resolution. We determined Cys107 ...Details: Incorporated TLS and nucleic acid secondary structure restraints into refinement and made manual corrections to improve overall model geometry and clash resolution. We determined Cys107 underwent chemical modification in both chains as evidenced by the difference peak map. These modifications were incorporated into the revised coordinate file.
Provider: author / Type: Coordinate replacement

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TetR family transcriptional regulator CifR
B: TetR family transcriptional regulator CifR
C: DNA (26-MER)
D: DNA (26-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,0875
Polymers59,9954
Non-polymers921
Water57632
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Gel filtration results indicate the protein alone is a dimer., native gel electrophoresis, EMSA results indicate the protein dimer could form complex with 26bp double-strand ...Evidence: gel filtration, Gel filtration results indicate the protein alone is a dimer., native gel electrophoresis, EMSA results indicate the protein dimer could form complex with 26bp double-strand operator DNA in the following condition: 25mM HEPES, pH7.5 150mM NaCl 0.5mM DTT, SAXS, SAXS data shows the envelop of protein-DNA complex with a shape similar to the structures shown here.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9930 Å2
ΔGint-57 kcal/mol
Surface area22560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.968, 166.685, 82.979
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab

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Components

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TetR family transcriptional regulator ... , 2 types, 2 molecules AB

#1: Protein TetR family transcriptional regulator CifR


Mass: 22005.965 Da / Num. of mol.: 1 / Mutation: C99T,C181R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: PA14_26140 / Plasmid: pET-16b / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta2 (DE3) / References: UniProt: A0A0H2ZCS5, UniProt: Q9HZR6*PLUS
#2: Protein TetR family transcriptional regulator CifR


Mass: 22021.965 Da / Num. of mol.: 1 / Mutation: C99T,C181R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: PA14_26140 / Plasmid: pET-16b / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta2 (DE3) / References: UniProt: A0A0H2ZCS5

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DNA chain , 2 types, 2 molecules CD

#3: DNA chain DNA (26-MER)


Mass: 7941.160 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Pseudomonas aeruginosa (bacteria)
#4: DNA chain DNA (26-MER)


Mass: 8026.255 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Pseudomonas aeruginosa (bacteria)

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Non-polymers , 2 types, 33 molecules

#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 32 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.75 Å3/Da / Density % sol: 67.2 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1 M Tris, pH 7.5, 0.2 M magnesium chloride, 16% PEG4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.979075 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jul 12, 2017
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979075 Å / Relative weight: 1
ReflectionResolution: 2.6→29.86 Å / Num. obs: 28053 / % possible obs: 99.8 % / Redundancy: 12.2 % / Biso Wilson estimate: 66.44 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.1071 / Rpim(I) all: 0.03184 / Rrim(I) all: 0.1119 / Net I/σ(I): 17.92
Reflection shellResolution: 2.6→2.6929 Å / Redundancy: 12.7 % / Rmerge(I) obs: 1.312 / Num. unique obs: 2765 / CC1/2: 0.723 / CC star: 0.916 / Rpim(I) all: 0.3793 / Rrim(I) all: 1.367 / % possible all: 99.89

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 6NSR

6nsr


Resolution: 2.6→29.86 Å / SU ML: 0.3862 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 25.3845
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2416 1419 5.06 %
Rwork0.2228 26609 -
obs0.2238 28028 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 74.48 Å2
Refinement stepCycle: LAST / Resolution: 2.6→29.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3029 1060 6 32 4127
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064295
X-RAY DIFFRACTIONf_angle_d0.82526027
X-RAY DIFFRACTIONf_chiral_restr0.0514659
X-RAY DIFFRACTIONf_plane_restr0.0075614
X-RAY DIFFRACTIONf_dihedral_angle_d22.57621685
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.690.39651420.37482621X-RAY DIFFRACTION99.89
2.69-2.80.27521420.28722606X-RAY DIFFRACTION100
2.8-2.930.30611420.25362622X-RAY DIFFRACTION99.96
2.93-3.080.31781420.24572636X-RAY DIFFRACTION100
3.08-3.270.27981410.25322604X-RAY DIFFRACTION99.46
3.28-3.530.25061420.21172647X-RAY DIFFRACTION99.96
3.53-3.880.24821420.1962655X-RAY DIFFRACTION100
3.88-4.440.20771420.1952661X-RAY DIFFRACTION99.93
4.44-5.590.19611420.20662709X-RAY DIFFRACTION99.96
5.59-29.860.2321420.22872848X-RAY DIFFRACTION99.73
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)
12.45987431156-0.5997087703741.753911532061.71092215774-0.2192906444932.8757928848-0.2190356029740.2686796353170.412238836174-0.2701875777270.0259468700012-0.0183402893372-0.5114785617450.2643886532830.1972077468180.494719270718-0.0607691037439-0.02788992119490.3718069301470.06262553772640.40085445284842.881828616252.561467595967.151423693
23.948462746860.6168270723922.312745020462.04254835770.2936554143062.894138747880.1566845644070.297223910449-0.590947689467-0.2562634139590.0700016021570.02932056248320.5372588050390.182946587275-0.2034449898460.4385106001790.0197376002527-0.004430900037940.324006889621-0.04956447163940.45386356147241.637091767928.568091207168.6881889029
31.62931867601-0.1014972972-0.1164358920671.215771786911.168530775891.066446420060.3928275304740.631419588832-0.274263223845-1.69530020017-0.5171922590151.411304066560.199105059354-0.2431041488990.1763543962681.28004158583-0.0230753273676-0.5633306760520.792281223081-0.1394391486151.0541316224317.841042286840.146481064244.5088907868
41.311218883310.0795588370541-0.06518203315910.72189999530.5697048725742.041812708190.2036911450990.501946012351-0.00244757365991-1.5111477982-0.4959248961071.728874015290.0723327087467-0.3203139801030.280496206191.078557984610.0642222855559-0.4985470128730.71949905539-0.0599256070851.1180096138216.971632511540.383436034245.4337536237
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11Chain AAA - B3 - 2011
22Chain BBC5 - 1961 - 192
33Chain CCD1 - 26
44Chain DDE1 - 26

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