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- PDB-7d3t: Crystal structure of OSPHR2 in complex with DNA -

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Basic information

Entry
Database: PDB / ID: 7d3t
TitleCrystal structure of OSPHR2 in complex with DNA
Components
  • DNA (5'-D(P*CP*TP*CP*GP*GP*AP*TP*AP*TP*CP*CP*TP*CP*AP*AP*G)-3')
  • DNA (5'-D(P*GP*CP*TP*TP*GP*AP*GP*GP*AP*TP*AP*TP*CP*CP*GP*A)-3')
  • Protein PHOSPHATE STARVATION RESPONSE 2
KeywordsDNA BINDING PROTEIN/DNA / Protein PHOSPHATE STARVATION RESPONSE 2 / MYB / DNA BINDING PROTEIN / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


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
DNA / DNA (> 10) / Protein PHOSPHATE STARVATION RESPONSE 2
Similarity search - Component
Biological speciesOryza sativa subsp. indica (long-grained rice)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsGuan, Z.Y. / Zhang, Z.F. / Liu, Z.
CitationJournal: Nat Commun / Year: 2022
Title: Mechanistic insights into the regulation of plant phosphate homeostasis by the rice SPX2 - PHR2 complex.
Authors: Guan, Z. / Zhang, Q. / Zhang, Z. / Zuo, J. / Chen, J. / Liu, R. / Savarin, J. / Broger, L. / Cheng, P. / Wang, Q. / Pei, K. / Zhang, D. / Zou, T. / Yan, J. / Yin, P. / Hothorn, M. / Liu, Z.
History
DepositionSep 20, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 6, 2021Provider: repository / Type: Initial release
Revision 1.1May 4, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
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 PHOSPHATE STARVATION RESPONSE 2
B: Protein PHOSPHATE STARVATION RESPONSE 2
C: Protein PHOSPHATE STARVATION RESPONSE 2
D: Protein PHOSPHATE STARVATION RESPONSE 2
E: DNA (5'-D(P*GP*CP*TP*TP*GP*AP*GP*GP*AP*TP*AP*TP*CP*CP*GP*A)-3')
F: DNA (5'-D(P*CP*TP*CP*GP*GP*AP*TP*AP*TP*CP*CP*TP*CP*AP*AP*G)-3')
G: DNA (5'-D(P*GP*CP*TP*TP*GP*AP*GP*GP*AP*TP*AP*TP*CP*CP*GP*A)-3')
H: DNA (5'-D(P*CP*TP*CP*GP*GP*AP*TP*AP*TP*CP*CP*TP*CP*AP*AP*G)-3')


Theoretical massNumber of molelcules
Total (without water)83,4838
Polymers83,4838
Non-polymers00
Water1629
1
A: Protein PHOSPHATE STARVATION RESPONSE 2
B: Protein PHOSPHATE STARVATION RESPONSE 2
E: DNA (5'-D(P*GP*CP*TP*TP*GP*AP*GP*GP*AP*TP*AP*TP*CP*CP*GP*A)-3')
F: DNA (5'-D(P*CP*TP*CP*GP*GP*AP*TP*AP*TP*CP*CP*TP*CP*AP*AP*G)-3')


Theoretical massNumber of molelcules
Total (without water)41,7424
Polymers41,7424
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5240 Å2
ΔGint-26 kcal/mol
Surface area11920 Å2
MethodPISA
2
C: Protein PHOSPHATE STARVATION RESPONSE 2
D: Protein PHOSPHATE STARVATION RESPONSE 2
G: DNA (5'-D(P*GP*CP*TP*TP*GP*AP*GP*GP*AP*TP*AP*TP*CP*CP*GP*A)-3')
H: DNA (5'-D(P*CP*TP*CP*GP*GP*AP*TP*AP*TP*CP*CP*TP*CP*AP*AP*G)-3')


Theoretical massNumber of molelcules
Total (without water)41,7424
Polymers41,7424
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5420 Å2
ΔGint-33 kcal/mol
Surface area11680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.414, 100.824, 79.351
Angle α, β, γ (deg.)90.000, 102.456, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein
Protein PHOSPHATE STARVATION RESPONSE 2 / OsPHR2


Mass: 15972.570 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryza sativa subsp. indica (long-grained rice)
Gene: PHR2, OsI_25821 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: B8B5N8
#2: DNA chain DNA (5'-D(P*GP*CP*TP*TP*GP*AP*GP*GP*AP*TP*AP*TP*CP*CP*GP*A)-3')


Mass: 4938.215 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(P*CP*TP*CP*GP*GP*AP*TP*AP*TP*CP*CP*TP*CP*AP*AP*G)-3')


Mass: 4858.167 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 9 / 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: 2.69 Å3/Da / Density % sol: 54.21 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / Details: PEG 3350, sodium malonate / PH range: 6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97854 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 7, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97854 Å / Relative weight: 1
ReflectionResolution: 2.7→49 Å / Num. obs: 45458 / % possible obs: 99.2 % / Redundancy: 3.4 % / Biso Wilson estimate: 66.73 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.07 / Rpim(I) all: 0.06 / Rrim(I) all: 0.084 / Net I/σ(I): 12
Reflection shellResolution: 2.7→2.83 Å / Mean I/σ(I) obs: 1.7 / Num. unique obs: 11093 / CC1/2: 0.704 / Rpim(I) all: 0.691

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6KVO

6kvo


Resolution: 2.7→49 Å / SU ML: 0.4526 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 35.5212
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2578 2289 5.04 %
Rwork0.2128 43169 -
obs0.2151 45458 94.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 79.63 Å2
Refinement stepCycle: LAST / Resolution: 2.7→49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1971 1309 0 9 3289
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01133480
X-RAY DIFFRACTIONf_angle_d1.37654963
X-RAY DIFFRACTIONf_chiral_restr0.058551
X-RAY DIFFRACTIONf_plane_restr0.0096400
X-RAY DIFFRACTIONf_dihedral_angle_d30.507898
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.750.45671240.4232666X-RAY DIFFRACTION92.91
2.75-2.820.44931610.41852748X-RAY DIFFRACTION96.26
2.82-2.890.47141480.40382725X-RAY DIFFRACTION96.15
2.89-2.970.37621700.37012728X-RAY DIFFRACTION96.5
2.97-3.050.32781700.32152699X-RAY DIFFRACTION94.84
3.05-3.150.38021180.31012630X-RAY DIFFRACTION93.03
3.15-3.270.33091430.28042643X-RAY DIFFRACTION92.74
3.27-3.40.26981390.25862666X-RAY DIFFRACTION93.03
3.4-3.550.32681590.22972614X-RAY DIFFRACTION93.87
3.55-3.740.26291510.20152777X-RAY DIFFRACTION96.57
3.74-3.970.2931270.19662724X-RAY DIFFRACTION95.86
3.97-4.280.24931320.182706X-RAY DIFFRACTION95.08
4.28-4.710.22331300.16942744X-RAY DIFFRACTION96.31
4.71-5.390.20571570.16652733X-RAY DIFFRACTION95.38
5.39-6.790.20371320.19072675X-RAY DIFFRACTION94.01
6.79-490.15441280.14692691X-RAY DIFFRACTION93.87
Refinement TLS params.Method: refined / Origin x: 12.0780878216 Å / Origin y: 31.198219914 Å / Origin z: 22.4408595758 Å
111213212223313233
T0.725098365684 Å20.0331348850754 Å20.126079846283 Å2-0.305352302769 Å2-0.0522019915559 Å2--0.6280846452 Å2
L1.15751767339 °20.292958640762 °2-0.397715606798 °2-1.36342696226 °2-0.34102894403 °2--1.41184860046 °2
S-0.124797586715 Å °0.171275504512 Å °-0.0271082800572 Å °-0.368383500188 Å °0.0807956650535 Å °0.169845779166 Å °0.121859020482 Å °-0.10602566561 Å °0.0906742938959 Å °
Refinement TLS groupSelection details: all

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