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- PDB-7yt9: crystal structure of AGD1-4 of Arabidopsis AGDP3 -

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Basic information

Entry
Database: PDB / ID: 7yt9
Titlecrystal structure of AGD1-4 of Arabidopsis AGDP3
ComponentsAGD1-4 of Arabidopsis AGDP3
KeywordsGENE REGULATION / AGENET domain / ROS1 / H3K9me2 binding
Function / homologyProtein of unknown function DUF724 / Protein of unknown function (DUF724) / Agenet domain, plant type / Tudor-like domain present in plant sequences. / Agenet-like domain / Agenet domain / nucleus / Agenet domain-containing protein
Function and homology information
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.6 Å
AuthorsZhou, X. / Du, J.
Funding support China, 1items
OrganizationGrant numberCountry
Other governmentJCYJ20200109110403829 China
CitationJournal: J Integr Plant Biol / Year: 2022
Title: The H3K9me2-binding protein AGDP3 limits DNA methylation and transcriptional gene silencing in Arabidopsis.
Authors: Zhou, X. / Wei, M. / Nie, W. / Xi, Y. / Peng, L. / Zheng, Q. / Tang, K. / Satheesh, V. / Wang, Y. / Luo, J. / Du, X. / Liu, R. / Yang, Z. / La, H. / Zhong, Y. / Yang, Y. / Zhu, J.K. / Du, J. / Lei, M.
History
DepositionAug 13, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 12, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 11, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: AGD1-4 of Arabidopsis AGDP3
B: AGD1-4 of Arabidopsis AGDP3


Theoretical massNumber of molelcules
Total (without water)66,7842
Polymers66,7842
Non-polymers00
Water1086
1
A: AGD1-4 of Arabidopsis AGDP3


Theoretical massNumber of molelcules
Total (without water)33,3921
Polymers33,3921
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: AGD1-4 of Arabidopsis AGDP3


Theoretical massNumber of molelcules
Total (without water)33,3921
Polymers33,3921
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)78.538, 129.205, 167.049
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number24
Space group name H-MI212121

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Components

#1: Protein AGD1-4 of Arabidopsis AGDP3


Mass: 33391.902 Da / Num. of mol.: 2 / Mutation: K261A,K262A,E263A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: DUF6, ATDUF6, At2g47230, T8I13.7 / Plasmid: pET-Sumo / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: F4IL23
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / 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: 3.17 Å3/Da / Density % sol: 61.23 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.1 M lithium sulfate, 20% PEG1000 and 0.1M sodium citrate, pH 5.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9789 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 13, 2018
RadiationMonochromator: silicon crystal (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 26390 / % possible obs: 99.2 % / Redundancy: 4.4 % / Biso Wilson estimate: 78.11 Å2 / Rmerge(I) obs: 0.039 / Rpim(I) all: 0.021 / Rrim(I) all: 0.045 / Χ2: 0.621 / Net I/σ(I): 10.6 / Num. measured all: 116578
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.6-2.694.50.70526110.8340.3680.7980.44399.7
2.69-2.84.60.45326170.9160.2330.5110.45499.7
2.8-2.934.60.28926170.9570.1490.3260.4699.7
2.93-3.084.40.16626150.9840.0880.1890.49899.9
3.08-3.284.10.126100.9910.0550.1150.57998.8
3.28-3.534.60.06926360.9950.0360.0780.67699.5
3.53-3.884.60.04626470.9970.0240.0530.72999.9
3.88-4.454.40.03126390.9980.0170.0360.79998.8
4.45-5.64.30.02726470.9990.0150.0310.79997.9
5.6-504.30.02427510.9990.0130.0280.78298.1

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
HKL-2000data scaling
PDB_EXTRACT3.27data extraction
HKL-3000data reduction
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.6→47.81 Å / SU ML: 0.43 / Cross valid method: THROUGHOUT / σ(F): 1.39 / Phase error: 31.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2722 1326 5.04 %
Rwork0.2447 25005 -
obs0.2461 26331 99.15 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 194.32 Å2 / Biso mean: 91.7452 Å2 / Biso min: 49.32 Å2
Refinement stepCycle: final / Resolution: 2.6→47.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4419 0 0 6 4425
Biso mean---78.47 -
Num. residues----544
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.6-2.70.36861440.349127392883100
2.7-2.830.42681400.379327732913100
2.83-2.980.43041500.379727532903100
2.98-3.160.30781650.311927332898100
3.16-3.410.33551450.29852759290499
3.41-3.750.31641630.284927752938100
3.75-4.290.30511190.22662815293499
4.29-5.410.21841600.19062749290998
5.41-47.810.20831400.21172909304998
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)
15.6359-0.41120.50378.6375-0.17847.9497-0.39870.03860.3772-0.81030.42520.1683-0.52790.3438-0.07670.8614-0.1371-0.07380.59510.04830.602216.008714.1464-56.4433
23.6761.6017-0.86763.7463-0.51618.41240.03190.1525-0.0032-0.36820.2092-0.2593-0.04580.6509-0.17450.4727-0.01280.07550.52140.03540.596618.094712.0955-47.4932
34.42740.2108-2.82311.5098-1.43936.49670.178-0.7665-0.11030.2628-0.06790.2334-0.20240.1429-0.29250.5998-0.05730.02050.4616-0.02780.54376.711413.9761-28.5619
44.9846-5.8789-4.07436.89565.85556.3276-0.2901-0.072-0.760.124-0.12280.65610.2536-0.18240.33040.5634-0.03340.07930.4730.05430.76412.74514.8311-31.7518
52.2627-1.73760.43757.4212-1.13877.9372-0.4699-0.89170.01831.75050.4448-0.1842-0.70530.0231-0.56910.7796-0.02990.16311.07280.05220.76273.40864.5964-9.9277
62.2347-1.68082.10848.7003-5.2564.889-0.1828-0.1489-0.61690.1530.74331.05420.0456-0.077-0.37720.97750.06820.20390.9160.19460.82142.8623-3.8755-7.0352
74.05830.6649-2.73046.3622-5.3848.89590.6240.0438-0.21310.9311-0.69060.3546-0.1977-0.07720.26890.9475-0.36330.20340.9873-0.33250.754847.75390.1105-21.4734
81.11690.3535-0.51474.3136-2.86213.36950.2955-0.45690.02720.8244-0.52350.8537-0.1813-0.09570.20430.756-0.16880.15491.0375-0.33680.820245.818.0325-28.5828
98.17342.6419-1.00877.6671-3.85564.98840.03850.1550.3949-0.3096-0.1789-0.3369-0.22260.46370.06360.50370.0057-0.05060.6080.04760.575465.888818.4616-51.4702
101.25991.1841-0.13272.9677-0.75981.6694-0.08560.03410.1177-0.2307-0.1760.0152-0.20450.01580.30360.68920.037-0.08690.6894-0.00090.645261.473318.21-53.5611
113.89990.4083-0.20655.57235.24485.3916-0.1405-0.0313-0.16020.2355-0.3938-0.02150.6277-0.33830.4370.7333-0.0725-0.07710.63150.11160.513261.240822.1004-68.725
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 29 )A4 - 29
2X-RAY DIFFRACTION2chain 'A' and (resid 30 through 132 )A30 - 132
3X-RAY DIFFRACTION3chain 'A' and (resid 133 through 180 )A133 - 180
4X-RAY DIFFRACTION4chain 'A' and (resid 181 through 205 )A181 - 205
5X-RAY DIFFRACTION5chain 'A' and (resid 206 through 229 )A206 - 229
6X-RAY DIFFRACTION6chain 'A' and (resid 230 through 284 )A230 - 284
7X-RAY DIFFRACTION7chain 'B' and (resid 4 through 29 )B4 - 29
8X-RAY DIFFRACTION8chain 'B' and (resid 30 through 154 )B30 - 154
9X-RAY DIFFRACTION9chain 'B' and (resid 155 through 180 )B155 - 180
10X-RAY DIFFRACTION10chain 'B' and (resid 181 through 229 )B181 - 229
11X-RAY DIFFRACTION11chain 'B' and (resid 230 through 284 )B230 - 284

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