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- PDB-7e40: Mechanism of Phosphate Sensing and Signaling Revealed by Rice SPX... -

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Basic information

Entry
Database: PDB / ID: 7.0E+40
TitleMechanism of Phosphate Sensing and Signaling Revealed by Rice SPX1-PHR2 Complex Structure
Components
  • Protein PHOSPHATE STARVATION RESPONSE 2
  • SPX domain-containing protein 1,Endolysin
KeywordsPROTEIN BINDING / phosphate sensing and responding / InsP6-OsSPX1-OsPHR2 ternary complex / allosterically regulation / DNA binding inhibition / PLANT PROTEIN
Function / homology
Function and homology information


positive regulation of cellular response to phosphate starvation / response to nitrate / regulation of phosphate transport / cellular response to phosphate starvation / cellular response to cold / viral release from host cell by cytolysis / peptidoglycan catabolic process / cell wall macromolecule catabolic process / lysozyme / lysozyme activity ...positive regulation of cellular response to phosphate starvation / response to nitrate / regulation of phosphate transport / cellular response to phosphate starvation / cellular response to cold / viral release from host cell by cytolysis / peptidoglycan catabolic process / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / host cell cytoplasm / defense response to bacterium / DNA-binding transcription factor activity / DNA binding / nucleus / cytoplasm
Similarity search - Function
SPX domain-containing protein / PHR1-like / MYB-CC type transcription factor, LHEQLE-containing domain / MYB-CC type transfactor, LHEQLE motif / SPX domain / Myb domain, plants / SPX domain / SPX domain profile. / Myb-type HTH DNA-binding domain profile. / Myb domain ...SPX domain-containing protein / PHR1-like / MYB-CC type transcription factor, LHEQLE-containing domain / MYB-CC type transfactor, LHEQLE motif / SPX domain / Myb domain, plants / SPX domain / SPX domain profile. / Myb-type HTH DNA-binding domain profile. / Myb domain / Myb-like DNA-binding domain / SANT/Myb domain / Endolysin T4 type / T4-type lysozyme / Glycoside hydrolase, family 24 / Lysozyme domain superfamily / Phage lysozyme / Homeobox-like domain superfamily / Lysozyme-like domain superfamily
Similarity search - Domain/homology
INOSITOL HEXAKISPHOSPHATE / Endolysin / SPX domain-containing protein 1 / Protein PHOSPHATE STARVATION RESPONSE 2
Similarity search - Component
Biological speciesOryza sativa subsp. japonica (Japanese rice)
Enterobacteria phage T4 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.6 Å
AuthorsZhou, J. / Hu, Q. / Yao, D. / Xing, W.
CitationJournal: Nat Commun / Year: 2021
Title: Mechanism of phosphate sensing and signaling revealed by rice SPX1-PHR2 complex structure.
Authors: Zhou, J. / Hu, Q. / Xiao, X. / Yao, D. / Ge, S. / Ye, J. / Li, H. / Cai, R. / Liu, R. / Meng, F. / Wang, C. / Zhu, J.K. / Lei, M. / Xing, W.
History
DepositionFeb 9, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 10, 2021Provider: repository / Type: Initial release
Revision 1.1Dec 15, 2021Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein PHOSPHATE STARVATION RESPONSE 2
B: SPX domain-containing protein 1,Endolysin
C: Protein PHOSPHATE STARVATION RESPONSE 2
D: SPX domain-containing protein 1,Endolysin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,7467
Polymers112,7664
Non-polymers1,9803
Water30617
1
A: Protein PHOSPHATE STARVATION RESPONSE 2
B: SPX domain-containing protein 1,Endolysin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,7034
Polymers56,3832
Non-polymers1,3202
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4560 Å2
ΔGint-32 kcal/mol
Surface area25550 Å2
MethodPISA
2
C: Protein PHOSPHATE STARVATION RESPONSE 2
D: SPX domain-containing protein 1,Endolysin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,0433
Polymers56,3832
Non-polymers6601
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3950 Å2
ΔGint-28 kcal/mol
Surface area25840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.244, 107.492, 174.521
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Protein PHOSPHATE STARVATION RESPONSE 2 / OsPHR2


Mass: 15554.029 Da / Num. of mol.: 2 / Mutation: V263M,L278M,L295M,L340M
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
#2: Protein SPX domain-containing protein 1,Endolysin / Protein SPX DOMAIN GENE 1 / OsSPX1 / Lysis protein / Lysozyme / Muramidase


Mass: 40828.941 Da / Num. of mol.: 2 / Mutation: C54T,C97A
Source method: isolated from a genetically manipulated source
Details: T4 lysozyme tagged OsSPX1,T4 lysozyme tagged OsSPX1
Source: (gene. exp.) Oryza sativa subsp. japonica (Japanese rice), (gene. exp.) Enterobacteria phage T4 (virus)
Gene: SPX1, Os06g0603600, LOC_Os06g40120, OsJ_21901, P0486H12.37, e, T4Tp126
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q69XJ0, UniProt: D9IEF7, lysozyme
#3: Chemical ChemComp-IHP / INOSITOL HEXAKISPHOSPHATE / MYO-INOSITOL HEXAKISPHOSPHATE / INOSITOL 1,2,3,4,5,6-HEXAKISPHOSPHATE / Phytic acid


Mass: 660.035 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H18O24P6 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 17 / 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: 2.71 Å3/Da / Density % sol: 54.67 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 8.6
Details: 0.1M Sodium phosphate dibasic/Citric acid pH 4.2, 10% PEG 3350, 0.2M NH4HCO3

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 1, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.6→45.76 Å / Num. obs: 38730 / % possible obs: 99.9 % / Redundancy: 7.042 % / Biso Wilson estimate: 56.956 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.099 / Rrim(I) all: 0.107 / Χ2: 1.339 / Net I/σ(I): 13.94
Reflection shellResolution: 2.6→2.75 Å / Redundancy: 6.787 % / Rmerge(I) obs: 0.715 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 11788 / CC1/2: 0.838 / Rrim(I) all: 0.775 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.18_3861refinement
XDSdata scaling
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.6→45.76 Å / SU ML: 0.38 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 28.29 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2741 1936 5 %
Rwork0.2257 36782 -
obs0.2281 38718 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 177.48 Å2 / Biso mean: 67.6555 Å2 / Biso min: 36.21 Å2
Refinement stepCycle: final / Resolution: 2.6→45.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7193 0 108 17 7318
Biso mean--158.67 57.17 -
Num. residues----885
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.6-2.660.32621360.28825692705100
2.66-2.730.30451360.273226012737100
2.73-2.810.33731350.265625692704100
2.81-2.90.32031360.273325842720100
2.9-3.010.31261370.270126092746100
3.01-3.130.36581370.256525932730100
3.13-3.270.31321370.257426122749100
3.27-3.440.32161370.24726072744100
3.44-3.660.30621380.237626192757100
3.66-3.940.25251380.217526252763100
3.94-4.340.27611400.205526532793100
4.34-4.960.25231390.193826432782100
4.96-6.250.2451420.227926952837100
6.25-45.760.20761480.19152803295199
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
15.5625-0.9647-0.40292.5158-5.81992.2856-0.2693-0.26850.2995-0.0274-0.0911-1.224-0.14690.42650.1120.50830.05620.00470.3922-0.03180.475149.476236.8897123.2217
24.459-0.7026-0.21929.61470.60195.3442-0.06560.43590.2711-0.2986-0.2905-1.5593-0.44020.68410.17170.30090.05510.03240.55690.07670.634955.075532.2467121.0642
32.22160.64621.0172.8249-1.27837.2530.2603-0.3922-0.18880.243-0.00860.1576-0.3429-0.32850.04340.2575-0.026-0.00890.3583-0.03110.496847.80524.0604135.1703
43.21890.10942.01042.2214-0.57524.1421-0.06-0.16740.11230.0739-0.1192-0.1055-0.2263-0.08420.11180.3201-0.02290.01690.28750.01770.441656.885413.1802131.4569
54.2411-1.79240.03332.44190.15454.14040.1563-0.0808-0.44050.08070.0396-0.19530.36010.8948-0.24420.4813-0.0196-0.1310.61010.01910.451220.7852-4.899111.4487
68.69670.0241-1.12722.32013.44249.4510.2306-0.0992-0.62460.5486-0.08080.59340.5344-0.2619-0.07170.49830.0677-0.02480.30050.06490.577947.1549-34.0473121.6127
74.35662.6501-2.2792.2213-1.75674.61130.12840.5190.5189-0.6160.11691.1524-0.4694-0.1711-0.03070.61010.2418-0.06990.5869-0.03090.636844.0038-23.0012114.9086
83.20030.3275-3.3711.62791.41312.17110.0419-0.4316-0.05490.1344-0.2913-0.25950.00170.82520.15460.3212-0.0353-0.03120.36050.03610.514352.2794-3.1026136.2545
93.3770.2843-0.17083.4064-0.31957.7804-0.0429-0.25640.26510.5303-0.22330.4782-0.1407-0.97410.08110.4023-0.09770.05520.3741-0.09420.557527.5274-9.8271145.644
101.9788-0.8001-0.61112.85611.53462.60450.08180.207-0.559-0.4047-0.4882-0.1293-0.21340.05260.08680.50550.02170.01490.3290.05920.411543.7651-17.3496125.6912
113.35270.1261-4.4172.4698-0.15147.6074-0.1698-0.1633-0.1693-0.1226-0.1854-0.09380.47590.10050.27860.3194-0.0286-0.05320.35250.01430.397147.2381-9.6639130.3912
124.809-1.46812.55797.0991-3.29887.28720.36980.5329-1.423-0.97050.01890.1151.73250.6579-0.60390.81240.0241-0.11490.5921-0.10180.736674.8934-16.418687.9893
133.9487-1.88222.59536.5618-2.80227.3234-0.4118-0.03050.17210.1420.22070.0887-0.7066-0.01930.15290.3977-0.0412-0.02170.41010.02080.289771.68635.362788.7576
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 248 through 281 )A248 - 281
2X-RAY DIFFRACTION2chain 'A' and (resid 282 through 330 )A282 - 330
3X-RAY DIFFRACTION3chain 'A' and (resid 331 through 376 )A331 - 376
4X-RAY DIFFRACTION4chain 'B' and (resid 0 through 193 )B0 - 193
5X-RAY DIFFRACTION5chain 'B' and (resid 194 through 357 )B194 - 357
6X-RAY DIFFRACTION6chain 'C' and (resid 247 through 287 )C247 - 287
7X-RAY DIFFRACTION7chain 'C' and (resid 288 through 333 )C288 - 333
8X-RAY DIFFRACTION8chain 'C' and (resid 334 through 375 )C334 - 375
9X-RAY DIFFRACTION9chain 'D' and (resid 13 through 66 )D13 - 66
10X-RAY DIFFRACTION10chain 'D' and (resid 67 through 113 )D67 - 113
11X-RAY DIFFRACTION11chain 'D' and (resid 114 through 192 )D114 - 192
12X-RAY DIFFRACTION12chain 'D' and (resid 193 through 255 )D193 - 255
13X-RAY DIFFRACTION13chain 'D' and (resid 256 through 357 )D256 - 357

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