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- PDB-6nsr: TetR family transcriptional regulator CifR C99T-C181R cysteine mu... -

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


DNA-binding transcription repressor activity / protein-DNA complex / transcription cis-regulatory region binding / negative regulation of DNA-templated transcription
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) / CifR
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3 Å
AuthorsHe, S. / Taher, N.M. / Simard, A.R. / Madden, D.R.
Funding support United States, 5items
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
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)T32 AI007519 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 1.1Jan 31, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description / Source and taxonomy / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author / database_2 / entity / entity_name_com / entity_src_gen / pdbx_unobs_or_zero_occ_atoms / struct_ncs_dom_lim / 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 / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _entity_src_gen.pdbx_gene_src_gene / _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 / _struct_ref.db_code / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_beg / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq.seq_align_beg
Revision 1.2Feb 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 / Polymer sequence / Refinement description / Source and taxonomy / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / audit_author / citation_author / entity / entity_poly / 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_instance_feature / pdbx_entry_details / pdbx_poly_seq_scheme / pdbx_refine_tls / pdbx_refine_tls_group / pdbx_related_exp_data_set / pdbx_struct_assembly_prop / pdbx_struct_mod_residue / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / pdbx_validate_torsion / refine / refine_hist / refine_ls_restr / refine_ls_shell / reflns / reflns_shell / software / struct_conf / struct_conn / struct_ncs_dom_lim / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _entity.pdbx_description / _entity_poly.pdbx_strand_id ..._entity.pdbx_description / _entity_poly.pdbx_strand_id / _entity_src_gen.gene_src_strain / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name / _ndb_struct_na_base_pair.buckle / _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_entry_details.has_ligand_of_interest / _pdbx_poly_seq_scheme.auth_mon_id / _pdbx_poly_seq_scheme.auth_seq_num / _pdbx_poly_seq_scheme.pdb_mon_id / _pdbx_poly_seq_scheme.pdb_strand_id / _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.overall_SU_ML / _refine.pdbx_ls_cross_valid_method / _refine.pdbx_overall_phase_error / _refine.pdbx_solvent_vdw_probe_radii / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_protein / _refine_ls_restr.dev_ideal / _refine_ls_restr.number / _refine_ls_shell.R_factor_R_free / _refine_ls_shell.R_factor_R_work / _refine_ls_shell.d_res_high / _refine_ls_shell.percent_reflns_obs / _reflns.pdbx_Rrim_I_all / _reflns.pdbx_netI_over_av_sigmaI / _reflns_shell.meanI_over_sigI_obs / _reflns_shell.pdbx_Rrim_I_all / _struct_ref.db_code / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_beg / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq.pdbx_strand_id / _struct_ref_seq.seq_align_beg / _struct_ref_seq_dif.db_mon_id / _struct_ref_seq_dif.details / _struct_ref_seq_dif.mon_id / _struct_ref_seq_dif.pdbx_auth_seq_num / _struct_ref_seq_dif.pdbx_pdb_strand_id / _struct_ref_seq_dif.pdbx_seq_db_accession_code / _struct_ref_seq_dif.pdbx_seq_db_seq_num / _struct_ref_seq_dif.seq_num
Description: Real space R-factor
Details: We performed further rounds of refinement by applying the TLS strategy for the protein and nucleic acid secondary structure constraints for DNA. We made manual corrections to improve overall ...Details: We performed further rounds of refinement by applying the TLS strategy for the protein and nucleic acid secondary structure constraints for DNA. We made manual corrections to improve overall model geometry and clash resolution. Due to weak electron density, we deleted the residues 96-118 of chain E.
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: CifR
B: CifR
C: DNA (26-MER)
D: DNA (26-MER)
E: CifR


Theoretical massNumber of molelcules
Total (without water)82,6415
Polymers82,6415
Non-polymers00
Water00
1
A: CifR
B: CifR
C: DNA (26-MER)
D: DNA (26-MER)


  • defined by author&software
  • Evidence: gel filtration, Gel filtration results indicate that protein alone (MSE labeled) is a dimer, native gel electrophoresis, EMSA of native protein (same construct but non-MSE labeled) shows ...Evidence: gel filtration, Gel filtration results indicate that protein alone (MSE labeled) is a dimer, native gel electrophoresis, EMSA of native protein (same construct but non-MSE labeled) shows the protein could bind to 26bp double-strand operator DNA.
  • 60.4 kDa, 4 polymers
  • Search similar-shape structures of this assembly by Omokage search (details)
Theoretical massNumber of molelcules
Total (without water)60,4164
Polymers60,4164
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9420 Å2
ΔGint-58 kcal/mol
Surface area22800 Å2
MethodPISA
2
E: CifR

E: CifR


Theoretical massNumber of molelcules
Total (without water)44,4492
Polymers44,4492
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Buried area2500 Å2
ΔGint-8 kcal/mol
Surface area18300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.517, 165.569, 81.529
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

#1: Protein CifR


Mass: 22224.439 Da / Num. of mol.: 3 / Mutation: C99T,C181R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: cifR, PA2931 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9HZR6
#2: DNA chain DNA (26-MER)


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


Mass: 8026.255 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Pseudomonas aeruginosa (bacteria)
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: 2.68 Å3/Da / Density % sol: 54.06 %
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, 11% PEG1000, 11% PEG8000

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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: 0.9788 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jul 12, 2017
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9788 Å / Relative weight: 1
ReflectionResolution: 3→19.98 Å / Num. obs: 17781 / % possible obs: 99.6 % / Redundancy: 7.1 % / Biso Wilson estimate: 91.53 Å2 / CC1/2: 0.998 / Rrim(I) all: 0.15 / Net I/av σ(I): 11.05 / Net I/σ(I): 9.29
Reflection shellResolution: 3→3.0808 Å / Mean I/σ(I) obs: 1.55 / Num. unique obs: 5878 / CC1/2: 0.793 / Rrim(I) all: 1.34

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XSCALEdata scaling
AutoSolphasing
Cootmodel building
RefinementMethod to determine structure: SAD / Resolution: 3→19.98 Å / SU ML: 0.4124 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 24.092
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.246 1779 10.01 %RANDOM
Rwork0.2194 16002 --
obs0.2221 17781 99.78 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 102.72 Å2
Refinement stepCycle: LAST / Resolution: 3→19.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4279 1066 0 0 5345
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00445545
X-RAY DIFFRACTIONf_angle_d0.60227708
X-RAY DIFFRACTIONf_chiral_restr0.0429845
X-RAY DIFFRACTIONf_plane_restr0.0044837
X-RAY DIFFRACTIONf_dihedral_angle_d18.77962153
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.080.39051350.37131211X-RAY DIFFRACTION99.85
3.08-3.170.36111350.29081211X-RAY DIFFRACTION99.56
3.17-3.270.30121290.25651182X-RAY DIFFRACTION98.72
3.27-3.390.29741350.26341209X-RAY DIFFRACTION99.48
3.39-3.520.31461370.25781219X-RAY DIFFRACTION99.78
3.52-3.680.28241360.24891226X-RAY DIFFRACTION100
3.68-3.880.26531340.21541209X-RAY DIFFRACTION100
3.88-4.120.22531360.20541220X-RAY DIFFRACTION100
4.12-4.430.22051370.19091236X-RAY DIFFRACTION100
4.43-4.870.21321380.19911242X-RAY DIFFRACTION99.86
4.87-5.560.2251370.22551238X-RAY DIFFRACTION100
5.57-6.960.24341420.24291274X-RAY DIFFRACTION100
6.97-19.980.21741480.18161325X-RAY DIFFRACTION99.93
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)
15.16126201775-1.871926578784.151675583542.17184916238-1.309560544915.14723777973-0.3479811024260.2497005040740.43054748304-0.1364324528180.0638187690312-0.0809674234561-0.5154576787620.2965422720550.2652107215940.44402113151-0.07462408179840.01134433279490.4253946705040.02110404465660.47954192553242.290974218352.145004016765.9174613171
24.906384432511.308992389343.577610846132.243766100440.6299680283025.089184857650.2403998892890.237686754985-0.538307813493-0.2798442206320.1128162795130.1104655176790.725279674530.0980795067025-0.3179734487230.5351919391430.0393907401779-0.002494235229410.42459915521-0.03318128424570.58602737428840.721342070328.450187414567.2338516436
31.26988260631-0.291930790912-0.6793845846295.038196399611.832468725221.482258049360.3849768857280.404791259334-0.0604932163308-2.0625548955-0.5691536298661.744024531520.0951981414379-0.3519372273040.1947153991921.30576375078-0.0440313836721-0.6223607448630.9442634380750.01290928169581.1615387195616.833114038240.917050106443.5547580884
41.17048370705-0.1561695571860.03387293214144.889029645181.089526703233.180973601530.3996233689020.415929331399-0.115799987429-1.37726381213-0.4806836972071.844886643250.304886486169-0.5232146730870.1118023452841.030269883160.0397198779082-0.4941760567910.873806125637-0.06207486323351.2799993058215.818659853640.685979341444.5273518606
51.744243257880.4892057815460.007426626279722.90873759442-1.864213683212.8711264487-0.316838520446-0.1558978892760.1498688806530.8920791051810.4409772421790.4867265805170.240950179373-0.608388009006-0.07320885129821.788424284860.1885772825780.1289685527860.9163386407320.09297910335171.0158574014620.97028180249.0869177053187.0914962629
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11Chain AAA5 - 1961 - 192
22Chain BBB6 - 1961 - 191
33Chain CCC1 - 26
44Chain DDD1 - 26
55Chain EEE10 - 1941 - 162

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