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- PDB-5w1e: PobR in complex with PHB -

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Basic information

Entry
Database: PDB / ID: 5w1e
TitlePobR in complex with PHB
ComponentsPutative transcriptional regulatorTranscriptional regulation
KeywordsTRANSCRIPTION / IclR / transcription factor
Function / homology
Function and homology information


DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / DNA binding
Similarity search - Function
helix_turn_helix isocitrate lyase regulation / Bacterial transcriptional regulator / Transcription regulator IclR, N-terminal / Transcription regulator IclR, C-terminal / IclR helix-turn-helix domain / IclR-type HTH domain profile. / IclR effector binding domain profile. / GAF-like domain superfamily / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
P-HYDROXYBENZOIC ACID / Putative transcriptional regulator
Similarity search - Component
Biological speciesStreptomyces coelicolor (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.06 Å
AuthorsPage, R. / Peti, W. / Lord, D.M. / Bajaj, R. / Zhang, R.
CitationJournal: Nucleic Acids Res. / Year: 2018
Title: A peculiar IclR family transcription factor regulates para-hydroxybenzoate catabolism in Streptomyces coelicolor.
Authors: Zhang, R. / Lord, D.M. / Bajaj, R. / Peti, W. / Page, R. / Sello, J.K.
History
DepositionJun 2, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 13, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2018Group: Author supporting evidence / Category: pdbx_audit_support
Revision 1.2May 16, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.3Oct 4, 2023Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,0435
Polymers55,6241
Non-polymers4184
Water6,900383
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, PHB-bound is monomeric
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1040 Å2
ΔGint-10 kcal/mol
Surface area21620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.134, 87.924, 69.915
Angle α, β, γ (deg.)90.00, 96.22, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Putative transcriptional regulator / Transcriptional regulation


Mass: 55624.434 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces coelicolor (strain ATCC BAA-471 / A3(2) / M145) (bacteria)
Strain: ATCC BAA-471 / A3(2) / M145 / Gene: SCO3209 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Z4X2
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-PHB / P-HYDROXYBENZOIC ACID / 4-Hydroxybenzoic acid


Mass: 138.121 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H6O3
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 383 / 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: 2.42 Å3/Da / Density % sol: 49.26 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 12% PEG MME 2000, 0.1 M MES, pH 5.8, 17.5 mM ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.54 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Feb 4, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.06→50 Å / Num. obs: 32727 / % possible obs: 99.7 % / Redundancy: 7.3 % / Rmerge(I) obs: 0.088 / Net I/σ(I): 26.6
Reflection shellResolution: 2.06→2.1 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.33 / Num. unique obs: 1568 / % possible all: 95.6

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575)refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIX(1.11.1_2575)phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2IA2

2ia2


Resolution: 2.06→32.319 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.38
RfactorNum. reflection% reflection
Rfree0.2062 1661 5.08 %
Rwork0.1642 --
obs0.1664 32696 99.41 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.06→32.319 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3674 0 27 383 4084
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023824
X-RAY DIFFRACTIONf_angle_d0.5485232
X-RAY DIFFRACTIONf_dihedral_angle_d10.6492341
X-RAY DIFFRACTIONf_chiral_restr0.041622
X-RAY DIFFRACTIONf_plane_restr0.004694
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0595-2.12010.2421360.18872426X-RAY DIFFRACTION93
2.1201-2.18860.22721320.18092597X-RAY DIFFRACTION100
2.1886-2.26680.26591220.17992585X-RAY DIFFRACTION100
2.2668-2.35750.22141570.18242573X-RAY DIFFRACTION100
2.3575-2.46470.20631500.16842597X-RAY DIFFRACTION100
2.4647-2.59460.22621420.18482588X-RAY DIFFRACTION100
2.5946-2.75710.22191310.18492586X-RAY DIFFRACTION100
2.7571-2.96990.22481310.18152599X-RAY DIFFRACTION100
2.9699-3.26850.26491310.18152616X-RAY DIFFRACTION100
3.2685-3.74080.18021540.15612591X-RAY DIFFRACTION100
3.7408-4.71070.17311350.13372619X-RAY DIFFRACTION100
4.7107-32.32260.17371400.14652658X-RAY DIFFRACTION100

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