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

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Basic information

Entry
Database: PDB / ID: 6toc
TitleCrystal structure of the oligomerisation domain of the transcription factor PHOSPHATE STARVATION RESPONSE 1 from Arabidopsis (crystal form 3).
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 / regulation of monoatomic ion transmembrane transport / cellular response to phosphate starvation / 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: 1.853 Å
AuthorsHothorn, M.
Funding support Switzerland, 2items
OrganizationGrant numberCountry
European Research Council (ERC)818696/INSPIRE Switzerland
Swiss National Science FoundationCRSII5_170925 Switzerland
Citation
Journal: 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.
#1: Journal: Acta Crystallogr D Biol Crystallogr / Year: 2010
Title: PHENIX: a comprehensive Python-based system for macromolecular structure solution.
Authors: Paul D Adams / Pavel V Afonine / Gábor Bunkóczi / Vincent B Chen / Ian W Davis / Nathaniel Echols / Jeffrey J Headd / Li-Wei Hung / Gary J Kapral / Ralf W Grosse-Kunstleve / Airlie J McCoy ...Authors: Paul D Adams / Pavel V Afonine / Gábor Bunkóczi / Vincent B Chen / Ian W Davis / Nathaniel Echols / Jeffrey J Headd / Li-Wei Hung / Gary J Kapral / Ralf W Grosse-Kunstleve / Airlie J McCoy / Nigel W Moriarty / Robert Oeffner / Randy J Read / David C Richardson / Jane S Richardson / Thomas C Terwilliger / Peter H Zwart /
Abstract: Macromolecular X-ray crystallography is routinely applied to understand biological processes at a molecular level. However, significant time and effort are still required to solve and complete many ...Macromolecular X-ray crystallography is routinely applied to understand biological processes at a molecular level. However, significant time and effort are still required to solve and complete many of these structures because of the need for manual interpretation of complex numerical data using many software packages and the repeated use of interactive three-dimensional graphics. PHENIX has been developed to provide a comprehensive system for macromolecular crystallographic structure solution with an emphasis on the automation of all procedures. This has relied on the development of algorithms that minimize or eliminate subjective input, the development of algorithms that automate procedures that are traditionally performed by hand and, finally, the development of a framework that allows a tight integration between the algorithms.
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 ...Data collection / Database references / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _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
AAA: Protein PHOSPHATE STARVATION RESPONSE 1
BBB: Protein PHOSPHATE STARVATION RESPONSE 1


Theoretical massNumber of molelcules
Total (without water)18,7452
Polymers18,7452
Non-polymers00
Water36020
1
AAA: Protein PHOSPHATE STARVATION RESPONSE 1
BBB: Protein PHOSPHATE STARVATION RESPONSE 1

AAA: Protein PHOSPHATE STARVATION RESPONSE 1
BBB: Protein PHOSPHATE STARVATION RESPONSE 1


Theoretical massNumber of molelcules
Total (without water)37,4914
Polymers37,4914
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Buried area7950 Å2
ΔGint-61 kcal/mol
Surface area10160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)31.523, 31.523, 81.599
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number77
Space group name H-MP42
Noncrystallographic symmetry (NCS)NCS domain: (Details: Chains AAA BBB)

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Components

#1: Protein Protein PHOSPHATE STARVATION RESPONSE 1 / AtPHR1


Mass: 9372.700 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 20 / 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

Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 0.1 M Bis-Tri pH 6.5, 0.1 M NaCl, 1.5 M (NH4)2SO4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.00004 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Jun 5, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00004 Å / Relative weight: 1
Reflection twin
TypeCrystal-IDIDOperatorDomain-IDFraction
pseudo-merohedral11H, K, L10.5053
pseudo-merohedral22-K, -H, -L20.4947
ReflectionResolution: 1.85→31.523 Å / Num. obs: 6769 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 13.5 % / CC1/2: 1 / Rrim(I) all: 0.073 / Net I/σ(I): 21.4
Reflection shellResolution: 1.85→1.97 Å / Mean I/σ(I) obs: 1 / Num. unique obs: 1072 / CC1/2: 0.4 / Rrim(I) all: 2.76 / % possible all: 99.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6TO5

6to5


Resolution: 1.853→31.5 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.934 / SU B: 2.66 / SU ML: 0.086 / Cross valid method: FREE R-VALUE / ESU R: 0.04 / ESU R Free: 0.037
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.265 334 4.936 %
Rwork0.2087 --
all0.211 --
obs-6767 99.882 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 38.292 Å2
Baniso -1Baniso -2Baniso -3
1-7.702 Å20 Å20 Å2
2--7.702 Å20 Å2
3----15.404 Å2
Refinement stepCycle: LAST / Resolution: 1.853→31.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms743 0 0 20 763
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.013760
X-RAY DIFFRACTIONr_bond_other_d0.0010.017739
X-RAY DIFFRACTIONr_angle_refined_deg1.21.6491010
X-RAY DIFFRACTIONr_angle_other_deg1.231.5761729
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.575589
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.52724.23152
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.13615179
X-RAY DIFFRACTIONr_dihedral_angle_4_deg28.606156
X-RAY DIFFRACTIONr_chiral_restr0.0590.293
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02823
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02139
X-RAY DIFFRACTIONr_nbd_refined0.210.2171
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1820.2637
X-RAY DIFFRACTIONr_nbtor_refined0.1490.2371
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.080.2349
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2730.211
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2370.234
X-RAY DIFFRACTIONr_nbd_other0.1930.2128
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.3380.23
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.1910.21
X-RAY DIFFRACTIONr_mcbond_it2.0733.748350
X-RAY DIFFRACTIONr_mcbond_other2.0643.74349
X-RAY DIFFRACTIONr_mcangle_it3.0845.599435
X-RAY DIFFRACTIONr_mcangle_other3.0845.607436
X-RAY DIFFRACTIONr_scbond_it3.2474.372409
X-RAY DIFFRACTIONr_scbond_other3.2444.37407
X-RAY DIFFRACTIONr_scangle_it5.0936.365573
X-RAY DIFFRACTIONr_scangle_other5.0946.366573
X-RAY DIFFRACTIONr_lrange_it6.66243.773856
X-RAY DIFFRACTIONr_lrange_other6.66743.832857
X-RAY DIFFRACTIONr_ncsr_local_group_10.1310.051298
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.853-1.9010.339330.306433X-RAY DIFFRACTION98.7288
1.901-1.9530.366240.287480X-RAY DIFFRACTION100
1.953-2.010.321190.266441X-RAY DIFFRACTION100
2.01-2.0720.301210.241442X-RAY DIFFRACTION100
2.072-2.1390.357160.215436X-RAY DIFFRACTION100
2.139-2.2140.225210.203398X-RAY DIFFRACTION100
2.214-2.2980.215230.185391X-RAY DIFFRACTION100
2.298-2.3910.199220.194382X-RAY DIFFRACTION100
2.391-2.4970.208200.237368X-RAY DIFFRACTION100
2.497-2.6180.224170.197367X-RAY DIFFRACTION100
2.618-2.7590.121130.221317X-RAY DIFFRACTION100
2.759-2.9260.256160.212325X-RAY DIFFRACTION100
2.926-3.1270.268160.219292X-RAY DIFFRACTION100
3.127-3.3760.35180.19275X-RAY DIFFRACTION100
3.376-3.6950.379110.173261X-RAY DIFFRACTION100
3.695-4.1270.354190.174223X-RAY DIFFRACTION100
4.127-4.7580.14690.146202X-RAY DIFFRACTION100
4.758-5.8070.05450.221180X-RAY DIFFRACTION99.4624
5.807-8.1310.27970.271139X-RAY DIFFRACTION100
8.131-31.50.58940.28381X-RAY DIFFRACTION98.8372

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