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- PDB-6j4r: Structural basis for the target DNA recognition and binding by th... -

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Basic information

Entry
Database: PDB / ID: 6j4r
TitleStructural basis for the target DNA recognition and binding by the MYB domain of phosphate starvation response regulator 1
Components
  • DNA (5'-D(*CP*AP*GP*TP*AP*TP*AP*TP*AP*CP*C)-3')
  • DNA (5'-D(*CP*CP*AP*TP*AP*TP*AP*TP*GP*AP*C)-3')
  • DNA (5'-D(*GP*GP*TP*AP*TP*AP*TP*AP*CP*TP*G)-3')
  • DNA (5'-D(*GP*TP*CP*AP*TP*AP*TP*AP*TP*GP*G)-3')
  • Protein PHOSPHATE STARVATION RESPONSE 1
KeywordsTRANSCRIPTION/DNA / MYB domain DNA / TRANSCRIPTION / TRANSCRIPTION-DNA complex
Function / homology
Function and homology information


response to arsenite ion / sulfate ion homeostasis / cellular response to high light intensity / cellular response to phosphate starvation / regulation of monoatomic ion transmembrane transport / circadian rhythm / DNA-binding transcription factor activity / regulation of DNA-templated transcription / DNA binding / nucleus
Similarity search - Function
: / MYB-CC type transcription factor, LHEQLE-containing domain / MYB-CC type transfactor, LHEQLE motif / Myb domain, plants / Myb-type HTH DNA-binding domain profile. / Myb domain / Myb-like DNA-binding domain / SANT/Myb domain / Homeodomain-like / Homeobox-like domain superfamily ...: / MYB-CC type transcription factor, LHEQLE-containing domain / MYB-CC type transfactor, LHEQLE motif / Myb domain, plants / Myb-type HTH DNA-binding domain profile. / Myb domain / Myb-like DNA-binding domain / SANT/Myb domain / Homeodomain-like / Homeobox-like domain superfamily / Arc Repressor Mutant, subunit A / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DNA / DNA (> 10) / Protein PHOSPHATE STARVATION RESPONSE 1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.8 Å
AuthorsJiang, M.Q. / Sun, L.F. / Isupov, M.N.
Funding support China, 1items
OrganizationGrant numberCountry
National Science Foundation (China)31470741 China
CitationJournal: Febs J. / Year: 2019
Title: Structural basis for the Target DNA recognition and binding by the MYB domain of phosphate starvation response 1.
Authors: Jiang, M. / Sun, L. / Isupov, M.N. / Littlechild, J.A. / Wu, X. / Wang, Q. / Wang, Q. / Yang, W. / Wu, Y.
History
DepositionJan 10, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 24, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 31, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Nov 20, 2019Group: Data collection / Category: reflns_shell / Item: _reflns_shell.Rmerge_I_obs
Revision 1.3Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: Protein PHOSPHATE STARVATION RESPONSE 1
B: Protein PHOSPHATE STARVATION RESPONSE 1
C: Protein PHOSPHATE STARVATION RESPONSE 1
D: Protein PHOSPHATE STARVATION RESPONSE 1
F: DNA (5'-D(*CP*CP*AP*TP*AP*TP*AP*TP*GP*AP*C)-3')
E: DNA (5'-D(*GP*TP*CP*AP*TP*AP*TP*AP*TP*GP*G)-3')
X: DNA (5'-D(*GP*GP*TP*AP*TP*AP*TP*AP*CP*TP*G)-3')
Y: DNA (5'-D(*CP*AP*GP*TP*AP*TP*AP*TP*AP*CP*C)-3')


Theoretical massNumber of molelcules
Total (without water)40,2028
Polymers40,2028
Non-polymers00
Water181
1
A: Protein PHOSPHATE STARVATION RESPONSE 1
D: Protein PHOSPHATE STARVATION RESPONSE 1
F: DNA (5'-D(*CP*CP*AP*TP*AP*TP*AP*TP*GP*AP*C)-3')
E: DNA (5'-D(*GP*TP*CP*AP*TP*AP*TP*AP*TP*GP*G)-3')


Theoretical massNumber of molelcules
Total (without water)20,1014
Polymers20,1014
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4540 Å2
ΔGint-14 kcal/mol
Surface area10100 Å2
MethodPISA
2
B: Protein PHOSPHATE STARVATION RESPONSE 1
C: Protein PHOSPHATE STARVATION RESPONSE 1
X: DNA (5'-D(*GP*GP*TP*AP*TP*AP*TP*AP*CP*TP*G)-3')
Y: DNA (5'-D(*CP*AP*GP*TP*AP*TP*AP*TP*AP*CP*C)-3')


Theoretical massNumber of molelcules
Total (without water)20,1014
Polymers20,1014
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4490 Å2
ΔGint-11 kcal/mol
Surface area9600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.966, 88.966, 143.445
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number94
Space group name H-MP42212

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Components

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DNA chain , 4 types, 4 molecules FEXY

#2: DNA chain DNA (5'-D(*CP*CP*AP*TP*AP*TP*AP*TP*GP*AP*C)-3')


Mass: 3317.199 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(*GP*TP*CP*AP*TP*AP*TP*AP*TP*GP*G)-3')


Mass: 3388.233 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: DNA chain DNA (5'-D(*GP*GP*TP*AP*TP*AP*TP*AP*CP*TP*G)-3')


Mass: 3388.233 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#5: DNA chain DNA (5'-D(*CP*AP*GP*TP*AP*TP*AP*TP*AP*CP*C)-3')


Mass: 3317.199 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Protein / Non-polymers , 2 types, 5 molecules ABCD

#1: Protein
Protein PHOSPHATE STARVATION RESPONSE 1 / AtPHR1


Mass: 6697.832 Da / Num. of mol.: 4 / Fragment: MYB domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: PHR1, At4g28610, T5F17.60 / Plasmid: pET32a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q94CL7
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / 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: 3.53 Å3/Da / Density % sol: 64.98 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 28%PEG3350 , 0.1M citrate-Na pH 5.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 4, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.8→75.61 Å / Num. obs: 14723 / % possible obs: 99.2 % / Redundancy: 12.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.111 / Rpim(I) all: 0.033 / Rrim(I) all: 0.116 / Net I/σ(I): 16
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.8-2.9513.24.07220820.6191.1574.23599.2
8.85-75.619.72.85620.9990.010.0399.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
xia2data scaling
PDB_EXTRACT3.24data extraction
xia2data reduction
PHENIXphasing
RefinementResolution: 2.8→71.72 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.954 / SU B: 19.322 / SU ML: 0.324 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.572 / ESU R Free: 0.313 / Details: U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2491 720 4.9 %RANDOM
Rwork0.2154 ---
obs0.2171 13959 99.05 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 222.95 Å2 / Biso mean: 102.85 Å2 / Biso min: 50.94 Å2
Baniso -1Baniso -2Baniso -3
1-6.16 Å20 Å20 Å2
2--6.16 Å20 Å2
3----12.32 Å2
Refinement stepCycle: final / Resolution: 2.8→71.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1821 886 0 1 2708
Biso mean---50.94 -
Num. residues----271
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0112851
X-RAY DIFFRACTIONr_angle_refined_deg1.6291.4674023
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1535223
X-RAY DIFFRACTIONr_dihedral_angle_2_deg23.64619.14994
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.24715352
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.9411518
X-RAY DIFFRACTIONr_chiral_restr0.0880.2367
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021826
LS refinement shellResolution: 2.8→2.872 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.532 49 -
Rwork0.499 1007 -
all-1056 -
obs--98.78 %

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