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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 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsHe, S. / Madden, D.R.
Funding support United States, 3items
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
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. / 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

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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
Water27015
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 area9760 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.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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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 (strain UCBPP-PA14) (bacteria)
Strain: UCBPP-PA14 / Gene: PA14_26140 / Production host: Escherichia coli (E. coli) / 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.: 15 / 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→27.983 Å / Num. obs: 22677 / % possible obs: 99.83 % / Redundancy: 13.5 % / Biso Wilson estimate: 69.9 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.163 / Net I/σ(I): 14.15
Reflection shellResolution: 2.8→2.9 Å / Num. unique obs: 4159 / CC1/2: 0.733

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 6NSN

6nsn


Resolution: 2.8→27.983 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 29.1
RfactorNum. reflection% reflection
Rfree0.2555 1158 5.11 %
Rwork0.2271 --
obs0.2286 22677 99.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.8→27.983 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3024 1060 0 15 4099
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0094294
X-RAY DIFFRACTIONf_angle_d1.0166029
X-RAY DIFFRACTIONf_dihedral_angle_d14.2833105
X-RAY DIFFRACTIONf_chiral_restr0.049661
X-RAY DIFFRACTIONf_plane_restr0.006614
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8001-2.92740.34561160.29272666X-RAY DIFFRACTION100
2.9274-3.08160.32981740.29682629X-RAY DIFFRACTION100
3.0816-3.27440.31741140.24812646X-RAY DIFFRACTION99
3.2744-3.52670.28331740.23112621X-RAY DIFFRACTION100
3.5267-3.88080.25241160.21062710X-RAY DIFFRACTION100
3.8808-4.44040.25051740.2042649X-RAY DIFFRACTION100
4.4404-5.58720.25721160.21842763X-RAY DIFFRACTION100
5.5872-27.98420.21571740.22692835X-RAY DIFFRACTION100

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