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- PDB-5fry: crystal structure of the phenol-responsive sensory domain of the ... -

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Basic information

Entry
Database: PDB / ID: 5fry
Titlecrystal structure of the phenol-responsive sensory domain of the transcription activator PoxR with 3,5-dimethylphenol
ComponentsPositive phenol-degradative gene regulator
KeywordsTRANSCRIPTION / PHENOL / DMPR / ENHANCER-BINDING PROTEIN / ACTIVATOR / ATPASE FAMILY
Function / homology
Function and homology information


sequence-specific DNA binding / regulation of DNA-templated transcription / ATP hydrolysis activity / ATP binding / metal ion binding / identical protein binding
Similarity search - Function
Activator of aromatic catabolism / Activator of aromatic catabolism / 4-vinyl reductase, 4VR / V4R domain / V4R / Sigma-54 interaction domain ATP-binding region A signature. / Sigma-54 interaction domain, conserved site / Sigma-54 interaction domain C-terminal part signature. / Sigma-54 interaction domain, ATP-binding site 1 / Sigma-54 interaction domain, ATP-binding site 2 ...Activator of aromatic catabolism / Activator of aromatic catabolism / 4-vinyl reductase, 4VR / V4R domain / V4R / Sigma-54 interaction domain ATP-binding region A signature. / Sigma-54 interaction domain, conserved site / Sigma-54 interaction domain C-terminal part signature. / Sigma-54 interaction domain, ATP-binding site 1 / Sigma-54 interaction domain, ATP-binding site 2 / Sigma-54 interaction domain ATP-binding region B signature. / Sigma-54 interaction domain profile. / NO signalling/Golgi transport ligand-binding domain superfamily / Sigma-54 interaction domain / RNA polymerase sigma factor 54 interaction domain / DNA binding HTH domain, Fis-type / Bacterial regulatory protein, Fis family / Homeobox-like domain superfamily / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
3,4-DIMETHYLPHENOL / Positive phenol-degradative gene regulator
Similarity search - Component
Biological speciesRalstonia sp. E2 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.792 Å
AuthorsPatil, V.V. / Woo, E.J.
CitationJournal: Structure / Year: 2016
Title: Structural Analysis of the Phenol-Responsive Sensory Domain of the Transcription Activator Poxr
Authors: Patil, V.V. / Park, K.-H. / Lee, S.-G. / Woo, E.J.
History
DepositionDec 23, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 18, 2016Provider: repository / Type: Initial release
Revision 2.0May 8, 2024Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Other / Source and taxonomy / Structure summary
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / entity / entity_name_com / entity_src_gen / pdbx_database_status / reflns / struct_ref / struct_site
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _entity_src_gen.gene_src_strain / _entity_src_gen.pdbx_beg_seq_num / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain / _entity_src_gen.pdbx_seq_type / _entity_src_gen.plasmid_name / _pdbx_database_status.status_code_sf / _reflns.d_resolution_low / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_seq_one_letter_code / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Positive phenol-degradative gene regulator
B: Positive phenol-degradative gene regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,3656
Polymers46,9902
Non-polymers3754
Water1,13563
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4440 Å2
ΔGint-35.4 kcal/mol
Surface area15820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.730, 70.696, 105.141
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Positive phenol-degradative gene regulator


Mass: 23495.096 Da / Num. of mol.: 2 / Fragment: PHENOL BINDING DOMAIN, UNP RESIDUES 1-211
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ralstonia sp. E2 (bacteria) / Gene: poxR / Plasmid: pET22B-CPD / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O84957
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-ERH / 3,4-DIMETHYLPHENOL


Mass: 122.164 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H10O
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 63 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 1.81 Å3/Da / Density % sol: 31.94 % / Description: NONE

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Data collection

DiffractionMean temperature: 287 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.97934
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 1.8→28.191 Å / Num. obs: 33213 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Redundancy: 13.8 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 55.11
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 11.5 % / Rmerge(I) obs: 0.68 / Mean I/σ(I) obs: 2.33 / % possible all: 99

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Processing

SoftwareName: PHENIX / Version: (PHENIX.REFINE: 1.9_1692) / Classification: refinement
RefinementMethod to determine structure: MIR
Starting model: NONE

Resolution: 1.792→28.191 Å / SU ML: 0.21 / σ(F): 1.33 / Phase error: 38.67 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3199 1919 6 %
Rwork0.2645 --
obs0.268 32000 95.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.792→28.191 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3024 0 20 63 3107
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083108
X-RAY DIFFRACTIONf_angle_d1.0794188
X-RAY DIFFRACTIONf_dihedral_angle_d14.9141134
X-RAY DIFFRACTIONf_chiral_restr0.041444
X-RAY DIFFRACTIONf_plane_restr0.005540
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7922-1.8370.36851330.3012054X-RAY DIFFRACTION93
1.837-1.88660.5291360.36492096X-RAY DIFFRACTION94
1.8866-1.94210.66621050.58411695X-RAY DIFFRACTION77
1.9421-2.00480.49381300.36292071X-RAY DIFFRACTION94
2.0048-2.07640.38451420.31372226X-RAY DIFFRACTION100
2.0764-2.15950.51941410.31232196X-RAY DIFFRACTION100
2.1595-2.25780.49171320.41522110X-RAY DIFFRACTION94
2.2578-2.37680.34331310.31342099X-RAY DIFFRACTION94
2.3768-2.52560.35191430.28252237X-RAY DIFFRACTION100
2.5256-2.72040.3121440.26932239X-RAY DIFFRACTION100
2.7204-2.99390.29351440.2652236X-RAY DIFFRACTION100
2.9939-3.42650.30731450.25432260X-RAY DIFFRACTION99
3.4265-4.31460.26141450.2112262X-RAY DIFFRACTION98
4.3146-28.19460.24131480.19992300X-RAY DIFFRACTION95

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