+Open data
-Basic information
Entry | Database: PDB / ID: 7d3y | ||||||
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Title | Crystal structure of the osPHR2-osSPX2 complex | ||||||
Components |
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Keywords | DNA BINDING PROTEIN / Protein PHOSPHATE STARVATION RESPONSE 2 / MYB / SPX2 | ||||||
Function / homology | Function and homology information 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 | ||||||
Biological species | Oryza sativa subsp. indica (long-grained rice) Homo sapiens (human) Oryza sativa subsp. japonica (Japanese rice) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.11 Å | ||||||
Authors | Zhang, Q.X. / Guan, Z.Y. / Zuo, J.Q. / Zhang, Z.F. / Liu, Z. | ||||||
Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7d3y.cif.gz | 460.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7d3y.ent.gz | 322.2 KB | Display | PDB format |
PDBx/mmJSON format | 7d3y.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d3/7d3y ftp://data.pdbj.org/pub/pdb/validation_reports/d3/7d3y | HTTPS FTP |
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-Related structure data
Related structure data | 7d3tSC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | 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 | 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 | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.29 Å3/Da / Density % sol: 62.63 % |
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Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, hanging drop Details: Ammonium sulfate, Pentaerythritol ethoxylate, Tacsimate PH range: 7 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9792 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 18, 2019 / Details: 0.9792 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 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 shell | Resolution: 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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 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
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 147.49 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.11→48.38 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 26.7645188018 Å / Origin y: -60.0185349528 Å / Origin z: 24.513360751 Å
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Refinement TLS group | Selection details: all |