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- PDB-7d3y: Crystal structure of the osPHR2-osSPX2 complex -

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Basic information

Entry
Database: PDB / ID: 7d3y
TitleCrystal structure of the osPHR2-osSPX2 complex
Components
  • Protein PHOSPHATE STARVATION RESPONSE 2
  • SPX domain-containing protein 2,Isoform 1 of Core histone macro-H2A.1
KeywordsDNA BINDING PROTEIN / Protein PHOSPHATE STARVATION RESPONSE 2 / MYB / SPX2
Function / homology
Function and homology information


negative regulation of unidimensional cell growth / regulation of leaf development / response to nitrate / regulation of phosphate transport / cellular response to phosphate starvation / cellular response to cold / DNA-binding transcription factor activity / DNA binding / nucleus / cytoplasm
Similarity search - Function
SPX domain-containing protein / MYB-CC type transcription factor, LHEQLE-containing domain / : / MYB-CC type transfactor, LHEQLE motif / Myb domain, plants / SPX domain / SPX domain / SPX domain profile. / Myb-type HTH DNA-binding domain profile. / Myb domain ...SPX domain-containing protein / MYB-CC type transcription factor, LHEQLE-containing domain / : / MYB-CC type transfactor, LHEQLE motif / Myb domain, plants / SPX domain / SPX domain / SPX domain profile. / 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
INOSITOL HEXAKISPHOSPHATE / SPX domain-containing protein 2 / Isoform 1 of Core histone macro-H2A.1 / Protein PHOSPHATE STARVATION RESPONSE 2
Similarity search - Component
Biological speciesOryza sativa subsp. indica (long-grained rice)
Homo sapiens (human)
Oryza sativa subsp. japonica (Japanese rice)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.11 Å
AuthorsZhang, Q.X. / Guan, Z.Y. / Zuo, J.Q. / 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 21, 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: SPX domain-containing protein 2,Isoform 1 of Core histone macro-H2A.1
B: SPX domain-containing protein 2,Isoform 1 of Core histone macro-H2A.1
C: Protein PHOSPHATE STARVATION RESPONSE 2
D: Protein PHOSPHATE STARVATION RESPONSE 2
E: Protein PHOSPHATE STARVATION RESPONSE 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)138,6237
Polymers137,3035
Non-polymers1,3202
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19510 Å2
ΔGint-126 kcal/mol
Surface area46880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)147.812, 147.812, 143.287
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Space group name HallP322"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
#4: x-y,-y,-z+1/3
#5: -x,-x+y,-z+2/3
#6: y,x,-z

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Components

#1: Protein SPX domain-containing protein 2,Isoform 1 of Core histone macro-H2A.1 / Protein SPX DOMAIN GENE 2 / OsSPX2 / mH2A1 / Histone H2A.y / H2A/y / Medulloblastoma antigen MU-MB-50.205


Mass: 43437.926 Da / Num. of mol.: 2 / Fragment: macro domain
Source method: isolated from a genetically manipulated source
Details: Fusion protein of SPX2, linker and histone macroH2A1.1
Source: (gene. exp.) Oryza sativa subsp. indica (long-grained rice), (gene. exp.) Homo sapiens (human)
Gene: SPX2, OsI_06282, MACROH2A1, H2AFY / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A2X254, UniProt: O75367-2
#2: Protein Protein PHOSPHATE STARVATION RESPONSE 2 / OsPHR2


Mass: 16809.039 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryza sativa subsp. japonica (Japanese rice)
Gene: PHR2, Os07g0438800, LOC_Os07g25710, OSJNBa0026I22.19, P0443H10.4
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q6Z156
#3: Chemical ChemComp-IHP / INOSITOL HEXAKISPHOSPHATE / MYO-INOSITOL HEXAKISPHOSPHATE / INOSITOL 1,2,3,4,5,6-HEXAKISPHOSPHATE


Mass: 660.035 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H18O24P6

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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: 3.29 Å3/Da / Density % sol: 62.63 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop
Details: Ammonium sulfate, Pentaerythritol ethoxylate, Tacsimate
PH range: 7

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9792 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 18, 2019 / Details: 0.9792
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 3.11→48.38 Å / Num. obs: 32993 / % possible obs: 99.9 % / Redundancy: 19.8 % / Biso Wilson estimate: 123.72 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.049 / Rpim(I) all: 0.012 / Rrim(I) all: 0.051 / Net I/σ(I): 35.4
Reflection shellResolution: 3.11→3.28 Å / Rmerge(I) obs: 0.844 / Mean I/σ(I) obs: 4.7 / Num. unique obs: 4743 / CC1/2: 0.957 / Rpim(I) all: 0.188 / Rrim(I) all: 0.865

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7D3T

7d3t


Resolution: 3.11→48.38 Å / SU ML: 0.4359 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 33.1497
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2526 1665 5.05 %
Rwork0.2202 31279 -
obs0.2219 32944 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 147.49 Å2
Refinement stepCycle: LAST / Resolution: 3.11→48.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7321 0 72 0 7393
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00717512
X-RAY DIFFRACTIONf_angle_d0.562810110
X-RAY DIFFRACTIONf_chiral_restr0.50591144
X-RAY DIFFRACTIONf_plane_restr0.00291261
X-RAY DIFFRACTIONf_dihedral_angle_d13.76632876
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.11-3.20.32891250.31842579X-RAY DIFFRACTION99.52
3.2-3.30.39071340.31352572X-RAY DIFFRACTION99.85
3.3-3.420.30911580.28422549X-RAY DIFFRACTION100
3.42-3.560.3511390.25752572X-RAY DIFFRACTION99.85
3.56-3.720.34351500.26132559X-RAY DIFFRACTION99.96
3.72-3.920.29171560.25152589X-RAY DIFFRACTION99.93
3.92-4.160.3031470.24192566X-RAY DIFFRACTION100
4.16-4.480.23971160.20122659X-RAY DIFFRACTION100
4.48-4.930.1991160.21032619X-RAY DIFFRACTION100
4.93-5.650.26161080.22752651X-RAY DIFFRACTION100
5.65-7.110.2711620.25452628X-RAY DIFFRACTION100
7.11-48.380.21540.17672736X-RAY DIFFRACTION99.45
Refinement TLS params.Method: refined / Origin x: 26.7645188018 Å / Origin y: -60.0185349528 Å / Origin z: 24.513360751 Å
111213212223313233
T0.73523404754 Å2-0.0444160002655 Å20.0264935948258 Å2-0.762466742216 Å20.0567281683797 Å2--0.827567023858 Å2
L1.52237860252 °20.32673389976 °20.166297617369 °2-0.753395048911 °20.271051994208 °2--0.659020747221 °2
S-0.085346431827 Å °0.230610301783 Å °0.0387202874128 Å °-0.0332273861166 Å °0.0351566325008 Å °-0.236820818021 Å °-0.0495816243314 Å °0.116273825627 Å °0.0402204277483 Å °
Refinement TLS groupSelection details: all

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