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- PDB-6to5: Crystal structure of the oligomerisation domain of the transcript... -

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Basic information

Entry
Database: PDB / ID: 6to5
TitleCrystal structure of the oligomerisation domain of the transcription factor PHOSPHATE STARVATION RESPONSE 1 from Arabidopsis.
ComponentsProtein PHOSPHATE STARVATION RESPONSE 1
KeywordsTRANSCRIPTION / phosphate starvation / myb domain / coiled-coil domain / inositol pyrophosphate / plant nutrition
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 / Homeobox-like domain superfamily
Similarity search - Domain/homology
Protein PHOSPHATE STARVATION RESPONSE 1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.38 Å
AuthorsHothorn, M.
Funding support Switzerland, 2items
OrganizationGrant numberCountry
European Research Council (ERC)818696/INSPIRE Switzerland
Swiss National Science FoundationCRSII5_170925 Switzerland
CitationJournal: Nat Commun / Year: 2021
Title: Inositol pyrophosphates promote the interaction of SPX domains with the coiled-coil motif of PHR transcription factors to regulate plant phosphate homeostasis.
Authors: Ried, M.K. / Wild, R. / Zhu, J. / Pipercevic, J. / Sturm, K. / Broger, L. / Harmel, R.K. / Abriata, L.A. / Hothorn, L.A. / Fiedler, D. / Hiller, S. / Hothorn, M.
History
DepositionDec 11, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 13, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 27, 2021Group: 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_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jan 24, 2024Group: 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

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Assembly

Deposited unit
AAAA: Protein PHOSPHATE STARVATION RESPONSE 1
AAAB: Protein PHOSPHATE STARVATION RESPONSE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,6563
Polymers18,6312
Non-polymers241
Water28816
1
AAAA: Protein PHOSPHATE STARVATION RESPONSE 1
AAAB: Protein PHOSPHATE STARVATION RESPONSE 1
hetero molecules

AAAA: Protein PHOSPHATE STARVATION RESPONSE 1
AAAB: Protein PHOSPHATE STARVATION RESPONSE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,3116
Polymers37,2634
Non-polymers492
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_565x,x-y+1,-z+1/61
Buried area10470 Å2
ΔGint-78 kcal/mol
Surface area12550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.400, 70.400, 148.880
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Space group name HallP612(x,y,z+5/12)
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/6
#3: y,-x+y,z+5/6
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+2/3
#8: -x,-y,z+1/2
#9: y,x,-z+1/3
#10: -y,-x,-z+5/6
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+1/6

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Components

#1: Protein Protein PHOSPHATE STARVATION RESPONSE 1 / AtPHR1


Mass: 9315.647 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: PHR1, At4g28610, T5F17.60 / Plasmid: pMH-HT / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): RIL / References: UniProt: Q94CL7
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 16 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.86 Å3/Da / Density % sol: 56.97 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.2
Details: 0.1 M phosphate citrate pH 4.2, 0.2 M NaCl, 20% (w/v) PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Dec 19, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.38→47.18 Å / Num. obs: 16576 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 20.8 % / Biso Wilson estimate: 48.58 Å2 / CC1/2: 1 / Rrim(I) all: 0.189 / Net I/σ(I): 14.9
Reflection shellResolution: 2.38→2.52 Å / Mean I/σ(I) obs: 1.48 / Num. unique obs: 2262 / CC1/2: 0.69 / Rrim(I) all: 2.21 / % possible all: 98.8

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
PHENIX1.16_3549refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5IIT

5iit


Resolution: 2.38→47.17 Å / SU ML: 0.2965 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.0838
RfactorNum. reflection% reflection
Rfree0.2294 826 4.99 %
Rwork0.2144 --
obs0.2153 16560 99.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 64.43 Å2
Refinement stepCycle: LAST / Resolution: 2.38→47.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms940 0 1 16 957
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0037947
X-RAY DIFFRACTIONf_angle_d0.59991260
X-RAY DIFFRACTIONf_chiral_restr0.0314139
X-RAY DIFFRACTIONf_plane_restr0.0031165
X-RAY DIFFRACTIONf_dihedral_angle_d7.8492603
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.38-2.530.28731350.27682617X-RAY DIFFRACTION99.24
2.53-2.720.27871380.24682617X-RAY DIFFRACTION99.93
2.72-30.26671350.24122617X-RAY DIFFRACTION100
3-3.430.28391370.22632627X-RAY DIFFRACTION100
3.43-4.320.18521380.19222631X-RAY DIFFRACTION100
4.32-47.170.21621430.20262625X-RAY DIFFRACTION100

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