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- PDB-6nsm: TetR family transcriptional regulator CifR C99T-C107S-C181R Cyste... -

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Basic information

Entry
Database: PDB / ID: 6nsm
TitleTetR family transcriptional regulator CifR C99T-C107S-C181R Cysteines mutant complexed with 26bp double-strand operator DNA
Components
  • (DNA (26-MER)) x 2
  • TetR family transcriptional regulator CifR
KeywordsTRANSCRIPTION/DNA / repressor / DNA-binding complex / epoxide sensing protein / 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 UCBPP-PA14 (bacteria)
Pseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 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 / Other / Refinement description / Source and taxonomy / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / audit_author / cell / citation_author / entity / entity_src_gen / ndb_struct_na_base_pair / ndb_struct_na_base_pair_step / pdbx_audit_support / pdbx_contact_author / pdbx_database_related / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_refine_tls / pdbx_refine_tls_group / pdbx_related_exp_data_set / pdbx_struct_assembly_prop / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / 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_conf / struct_conn / symmetry
Item: _cell.volume / _entity.pdbx_number_of_molecules ..._cell.volume / _entity.pdbx_number_of_molecules / _entity_src_gen.pdbx_gene_src_scientific_name / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_variant / _entity_src_gen.pdbx_host_org_vector_type / _entity_src_gen.plasmid_name / _pdbx_contact_author.address_2 / _pdbx_contact_author.id / _pdbx_contact_author.phone / _pdbx_poly_seq_scheme.auth_mon_id / _pdbx_poly_seq_scheme.auth_seq_num / _pdbx_poly_seq_scheme.pdb_mon_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.ls_d_res_low / _refine.ls_number_reflns_R_work / _refine.ls_number_reflns_obs / _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_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_netI_over_sigmaI / _reflns.percent_possible_obs / _reflns_shell.Rmerge_I_obs / _reflns_shell.meanI_over_sigI_obs / _reflns_shell.number_unique_obs / _reflns_shell.pdbx_CC_half / _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_auth_seq_id / _struct_conf.beg_label_comp_id / _struct_conf.beg_label_seq_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 / _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.
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)


Theoretical massNumber of molelcules
Total (without water)59,9154
Polymers59,9154
Non-polymers00
Water1267
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Gel filtration indicates the protein alone is a dimer., native gel electrophoresis, EMSA indicates the protein dimer could form complex with 26bp double-strand operator DNA ...Evidence: gel filtration, Gel filtration indicates the protein alone is a dimer., native gel electrophoresis, EMSA indicates the protein dimer could form complex with 26bp double-strand operator DNA at the following condition: 25mM HEPES pH7.5 150mM NaCl 0.5mM DTT (optional)
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9780 Å2
ΔGint-55 kcal/mol
Surface area22710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.329, 167.897, 82.538
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 TetR family transcriptional regulator CifR


Mass: 21973.900 Da / Num. of mol.: 2 / Mutation: C99T,C107S,C181R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa UCBPP-PA14 (bacteria)
Strain: UCBPP-PA14 / Gene: PA14_26140 / Plasmid: pET-16b / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta 2 (DE3) / References: UniProt: A0A0H2ZCS5, UniProt: Q9HZR6*PLUS
#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)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Formula: H2O

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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: 3.78 Å3/Da / Density % sol: 67.47 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.9
Details: 0.1 M Tris, pH 7.9, 0.2 M magnesium chloride, 18% PEG4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-2 / Wavelength: 0.979303 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 5, 2017
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979303 Å / Relative weight: 1
ReflectionResolution: 2.8→27.98 Å / Num. obs: 22709 / % possible obs: 99.68 % / Redundancy: 13.5 % / Biso Wilson estimate: 70.58 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.1588 / Rpim(I) all: 0.04456 / Rrim(I) all: 0.163 / Net I/σ(I): 15.16
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 14.1 % / Rmerge(I) obs: 1.623 / Mean I/σ(I) obs: 1.55 / Num. unique obs: 2226 / CC1/2: 0.654 / CC star: 0.889 / Rpim(I) all: 0.4435 / Rrim(I) all: 1.683 / % possible all: 100

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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 6NSN

6nsn


Resolution: 2.8→27.98 Å / SU ML: 0.3638 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.5013
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2478 1158 5.11 %
Rwork0.2277 21520 -
obs0.2288 22678 99.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 79.96 Å2
Refinement stepCycle: LAST / Resolution: 2.8→27.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3019 1060 0 7 4086
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00424285
X-RAY DIFFRACTIONf_angle_d0.56956014
X-RAY DIFFRACTIONf_chiral_restr0.0399657
X-RAY DIFFRACTIONf_plane_restr0.0045614
X-RAY DIFFRACTIONf_dihedral_angle_d22.63331684
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.930.35451160.30792666X-RAY DIFFRACTION100
2.93-3.080.34581740.31492629X-RAY DIFFRACTION99.96
3.08-3.270.28721140.24322647X-RAY DIFFRACTION99.17
3.27-3.530.25941740.23282621X-RAY DIFFRACTION99.79
3.53-3.880.22911160.21262710X-RAY DIFFRACTION99.96
3.88-4.440.22731740.20442649X-RAY DIFFRACTION100
4.44-5.590.24261160.21512763X-RAY DIFFRACTION100
5.59-27.980.23111740.22542835X-RAY DIFFRACTION99.77
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)
13.94651435354-1.046919564892.979351302472.27524946552-0.9412564337813.59768829125-0.2745551716190.2452907670770.492559873803-0.1723220533040.0418574771943-0.0109996033024-0.5168481965340.292357548740.2230832615330.462688877654-0.04599618628890.01280790370040.378574354851-0.0003319648870750.37785358259443.017494712452.958494257766.9253161022
23.188993291760.6956393448332.035480693261.926400874920.4761026659813.011766803890.1941673226440.258553555919-0.537842923596-0.2552420018880.05502347734980.1056927604730.5321251241390.200211521293-0.2233081119660.4752839421340.0497554200895-0.0006283755045720.385996695734-0.0501508546550.53887301100441.86774498229.049239335468.1002604177
31.897061239050.04765259313820.008966538673651.998689183311.221219271071.30175520040.3988910627730.693801143705-0.296326108965-1.70031469734-0.3477269965031.561043966010.256094249079-0.1986224635470.02573315112871.25074217853-0.0460899948791-0.5504773066490.770003416566-0.1004469431411.1441705759417.96066765340.912927453244.1211519576
41.47263818203-0.3201960709560.06131332233421.312767661680.670885856421.706203440830.2311130277360.398862009398-0.0183311876929-1.45662356475-0.5752013031151.591287874590.0553521256134-0.2833742533380.3408205417641.080331865620.0600601947423-0.4638219017330.776416561967-0.0834166393581.1111768683417.096869525841.162189710645.0016941888
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11Chain AAA4 - 1961 - 193
22Chain BBB5 - 1961 - 192
33Chain CCC1 - 26
44Chain DDD1 - 26

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