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- PDB-7xq5: Crystal structure of ScIno2p-ScIno4p bound promoter DNA -

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Basic information

Entry
Database: PDB / ID: 7xq5
TitleCrystal structure of ScIno2p-ScIno4p bound promoter DNA
Components
  • DNA (5'-D(*GP*AP*TP*TP*TP*TP*CP*AP*CP*AP*TP*GP*CP*AP*G)-3')
  • DNA (5'-D(P*CP*CP*TP*GP*CP*AP*TP*GP*TP*GP*AP*AP*AP*AP*T)-3')
  • Protein INO2
  • Protein INO4
KeywordsTRANSCRIPTION / Transcriptional regulators
Function / homology
Function and homology information


phospholipid biosynthetic process / RNA polymerase II transcription regulator complex / protein dimerization activity / positive regulation of transcription by RNA polymerase II / DNA binding / nucleus
Similarity search - Function
helix loop helix domain / Myc-type, basic helix-loop-helix (bHLH) domain / Myc-type, basic helix-loop-helix (bHLH) domain profile. / Helix-loop-helix DNA-binding domain superfamily
Similarity search - Domain/homology
HEXANE-1,6-DIOL / DNA / DNA (> 10) / Protein INO4 / Protein INO2
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsKhan, M.H. / Lu, X.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Int J Mol Sci / Year: 2022
Title: Structural Analysis of Ino2p/Ino4p Mutual Interactions and Their Binding Interface with Promoter DNA.
Authors: Khan, M.H. / Xue, L. / Yue, J. / Schuller, H.J. / Zhu, Z. / Niu, L.
History
DepositionMay 6, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 20, 2022Provider: repository / Type: Initial release
Revision 1.1Aug 10, 2022Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein INO4
B: Protein INO2
C: DNA (5'-D(P*CP*CP*TP*GP*CP*AP*TP*GP*TP*GP*AP*AP*AP*AP*T)-3')
D: DNA (5'-D(*GP*AP*TP*TP*TP*TP*CP*AP*CP*AP*TP*GP*CP*AP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,1757
Polymers26,8214
Non-polymers3553
Water1,38777
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry, Gel filtration, Electrophoretic mobility shift assay (EMSA)
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8030 Å2
ΔGint-52 kcal/mol
Surface area13480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.893, 97.893, 89.780
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Space group name HallP312"

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein Protein INO4


Mass: 8996.399 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: S288c / Gene: INO4 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P13902
#2: Protein Protein INO2


Mass: 8647.195 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: S288c / Gene: INO2 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P26798

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DNA chain , 2 types, 2 molecules CD

#3: DNA chain DNA (5'-D(P*CP*CP*TP*GP*CP*AP*TP*GP*TP*GP*AP*AP*AP*AP*T)-3')


Mass: 4593.010 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Saccharomyces cerevisiae (brewer's yeast)
#4: DNA chain DNA (5'-D(*GP*AP*TP*TP*TP*TP*CP*AP*CP*AP*TP*GP*CP*AP*G)-3')


Mass: 4583.997 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Saccharomyces cerevisiae (brewer's yeast)

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Non-polymers , 2 types, 80 molecules

#5: Chemical ChemComp-HEZ / HEXANE-1,6-DIOL


Mass: 118.174 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H14O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 77 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 4.59 Å3/Da / Density % sol: 73.22 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, sitting drop
Details: 0.01 M Cobalt (II) chloride hexahydrate, 0.1 M sodium acetate trihydrate, pH 5.0, 1.2 M 1, 6-hexandiol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97847 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 7, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97847 Å / Relative weight: 1
ReflectionResolution: 2.25→48.95 Å / Num. obs: 23995 / % possible obs: 99.42 % / Redundancy: 19.4 % / Biso Wilson estimate: 48.71 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.073 / Rpim(I) all: 0.017 / Rrim(I) all: 0.043 / Net I/σ(I): 30.3
Reflection shellResolution: 2.25→2.33 Å / Rmerge(I) obs: 1.592 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 2327 / CC1/2: 0.769 / Rpim(I) all: 0.374 / Rrim(I) all: 1.393 / % possible all: 98.27

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
HKL-2000data reduction
MOLREPphasing
BUCCANEERmodel building
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5GNJ

5gnj


Resolution: 2.25→48.95 Å / SU ML: 0.283 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.0213
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2346 1205 5.05 %
Rwork0.2137 22651 -
obs0.2148 23856 99.43 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 53.14 Å2
Refinement stepCycle: LAST / Resolution: 2.25→48.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1236 611 24 77 1948
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00841959
X-RAY DIFFRACTIONf_angle_d1.04532749
X-RAY DIFFRACTIONf_chiral_restr0.0463308
X-RAY DIFFRACTIONf_plane_restr0.0073242
X-RAY DIFFRACTIONf_dihedral_angle_d23.5912818
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.25-2.340.34341320.31942435X-RAY DIFFRACTION98.5
2.34-2.450.33191230.27462476X-RAY DIFFRACTION98.6
2.45-2.580.29741070.28212508X-RAY DIFFRACTION99.54
2.58-2.740.31961370.29312495X-RAY DIFFRACTION99.4
2.74-2.950.31271240.28152520X-RAY DIFFRACTION99.74
2.95-3.240.27731380.23562513X-RAY DIFFRACTION99.66
3.24-3.710.22841540.20492488X-RAY DIFFRACTION99.62
3.71-4.680.19241480.17482549X-RAY DIFFRACTION100
4.68-48.950.18531420.17762667X-RAY DIFFRACTION99.93

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