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- PDB-6o19: Crystal Structure of Pho7 complex with pho1 promoter site 2 -

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Basic information

Entry
Database: PDB / ID: 6o19
TitleCrystal Structure of Pho7 complex with pho1 promoter site 2
Components
  • DNA (5'-D(*GP*TP*TP*TP*TP*TP*AP*AP*TP*TP*TP*CP*CP*GP*AP*AP*TP*AP*AP*T)-3')
  • DNA (5'-D(*TP*TP*AP*TP*TP*CP*GP*GP*AP*AP*AP*TP*TP*AP*AP*AP*AP*AP*CP*A)-3')
  • Transcription factor Pho7
KeywordsTRANSCRIPTION/DNA / Zn2Cys6 / Zinc binuclear cluster transcription factor / transcription factor-DNA complex / Pho7 / TRANSCRIPTION / TRANSCRIPTION-DNA complex
Function / homology
Function and homology information


intracellular phosphate ion homeostasis / cellular response to phosphate starvation / RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding / cellular response to starvation / RNA polymerase II transcription regulatory region sequence-specific DNA binding / DNA-binding transcription activator activity, RNA polymerase II-specific / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / chromatin ...intracellular phosphate ion homeostasis / cellular response to phosphate starvation / RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding / cellular response to starvation / RNA polymerase II transcription regulatory region sequence-specific DNA binding / DNA-binding transcription activator activity, RNA polymerase II-specific / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / chromatin / positive regulation of transcription by RNA polymerase II / zinc ion binding / nucleus / cytosol
Similarity search - Function
Zn(2)-C6 fungal-type DNA-binding domain superfamily / Zn(2)-C6 fungal-type DNA-binding domain profile. / GAL4-like Zn(II)2Cys6 (or C6 zinc) binuclear cluster DNA-binding domain / Zn(2)-C6 fungal-type DNA-binding domain
Similarity search - Domain/homology
DNA / DNA (> 10) / Uncharacterized transcriptional regulatory protein C27B12.11c
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.596 Å
AuthorsGarg, A. / Goldgur, Y. / Shuman, S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)R35 GM126945 United States
CitationJournal: Mol.Cell.Biol. / Year: 2019
Title: Structure of Fission Yeast Transcription Factor Pho7 Bound topho1Promoter DNA and Effect of Pho7 Mutations on DNA Binding and Phosphate Homeostasis.
Authors: Garg, A. / Goldgur, Y. / Sanchez, A.M. / Schwer, B. / Shuman, S.
History
DepositionFeb 18, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 24, 2019Provider: repository / Type: Initial release
Revision 1.1May 8, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.2Jun 26, 2019Group: Data collection / Database references / Category: citation / Item: _citation.journal_volume / _citation.title
Revision 1.3Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 11, 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: Transcription factor Pho7
C: DNA (5'-D(*TP*TP*AP*TP*TP*CP*GP*GP*AP*AP*AP*TP*TP*AP*AP*AP*AP*AP*CP*A)-3')
B: DNA (5'-D(*GP*TP*TP*TP*TP*TP*AP*AP*TP*TP*TP*CP*CP*GP*AP*AP*TP*AP*AP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,1565
Polymers19,0253
Non-polymers1312
Water6,954386
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4950 Å2
ΔGint-19 kcal/mol
Surface area10350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.169, 37.581, 57.564
Angle α, β, γ (deg.)90.00, 104.23, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Transcription factor Pho7


Mass: 6763.157 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast)
Gene: pi067, SPBC27B12.11c / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O13658
#2: DNA chain DNA (5'-D(*TP*TP*AP*TP*TP*CP*GP*GP*AP*AP*AP*TP*TP*AP*AP*AP*AP*AP*CP*A)-3')


Mass: 6149.043 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Schizosaccharomyces pombe (fission yeast)
#3: DNA chain DNA (5'-D(*GP*TP*TP*TP*TP*TP*AP*AP*TP*TP*TP*CP*CP*GP*AP*AP*TP*AP*AP*T)-3')


Mass: 6112.987 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Schizosaccharomyces pombe (fission yeast)
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 386 / 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: 2.93 Å3/Da / Density % sol: 58.02 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.1M Tris.HCl pH 8.0, 0.2M NaOAc, 35% PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 11, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.596→50 Å / Num. obs: 28959 / % possible obs: 97.9 % / Redundancy: 4 % / CC1/2: 1 / Rpim(I) all: 0.027 / Net I/σ(I): 29.7
Reflection shellResolution: 1.596→1.63 Å / Redundancy: 3.5 % / Mean I/σ(I) obs: 0.979 / Num. unique obs: 1429 / Rpim(I) all: 0.131 / % possible all: 95.1

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Processing

Software
NameVersionClassification
PHENIX(1.14_3211: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Starting model: 6.0E+33 / Resolution: 1.596→43.571 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.68
RfactorNum. reflection% reflection
Rfree0.2027 3790 6.9 %
Rwork0.1809 --
obs0.1824 28905 95.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.596→43.571 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms466 814 2 386 1668
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081383
X-RAY DIFFRACTIONf_angle_d1.0482026
X-RAY DIFFRACTIONf_dihedral_angle_d23.884712
X-RAY DIFFRACTIONf_chiral_restr0.05222
X-RAY DIFFRACTIONf_plane_restr0.009121
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5961-1.61630.24421320.2311567X-RAY DIFFRACTION79
1.6163-1.63750.24091210.23041810X-RAY DIFFRACTION89
1.6375-1.660.22071310.21311873X-RAY DIFFRACTION94
1.66-1.68370.2361360.19931857X-RAY DIFFRACTION95
1.6837-1.70880.23321650.19691915X-RAY DIFFRACTION95
1.7088-1.73550.20761200.19861860X-RAY DIFFRACTION96
1.7355-1.7640.24181410.19591957X-RAY DIFFRACTION97
1.764-1.79440.21171500.19331818X-RAY DIFFRACTION93
1.7944-1.8270.22341290.19481858X-RAY DIFFRACTION95
1.827-1.86210.23711480.18781973X-RAY DIFFRACTION98
1.8621-1.90020.24041420.19741929X-RAY DIFFRACTION97
1.9002-1.94150.19921570.2091899X-RAY DIFFRACTION97
1.9415-1.98660.20991420.20031947X-RAY DIFFRACTION97
1.9866-2.03630.22041410.19211918X-RAY DIFFRACTION98
2.0363-2.09140.25761320.19081946X-RAY DIFFRACTION96
2.0914-2.15290.21131440.18991878X-RAY DIFFRACTION96
2.1529-2.22240.24541440.19091850X-RAY DIFFRACTION94
2.2224-2.30180.21331390.19211986X-RAY DIFFRACTION99
2.3018-2.3940.24361490.19431882X-RAY DIFFRACTION98
2.394-2.50290.20731420.1962011X-RAY DIFFRACTION98
2.5029-2.63490.21811490.18281898X-RAY DIFFRACTION97
2.6349-2.79990.21621370.18921891X-RAY DIFFRACTION96
2.7999-3.01610.19051420.19621911X-RAY DIFFRACTION98
3.0161-3.31950.231430.18041923X-RAY DIFFRACTION96
3.3195-3.79960.15411410.15361984X-RAY DIFFRACTION98
3.7996-4.78610.14311370.13871888X-RAY DIFFRACTION96
4.7861-43.58730.15551360.15011933X-RAY DIFFRACTION97

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