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- PDB-5zwz: Crystal structure of Arabidopsis thaliana AGDP1 AGD34 -

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Basic information

Entry
Database: PDB / ID: 5zwz
TitleCrystal structure of Arabidopsis thaliana AGDP1 AGD34
ComponentsAgenet domain-containing protein
KeywordsGENE REGULATION / AGENET domain / AGDP1 / epigenetics / H3K9me2
Function / homology
Function and homology information


: / DNA methylation-dependent heterochromatin formation / chromosome, centromeric region / heterochromatin / methylated histone binding / histone reader activity / histone binding / nucleus
Similarity search - Function
Agenet domain, plant type / Tudor-like domain present in plant sequences. / Agenet-like domain / Agenet domain
Similarity search - Domain/homology
Protein AGENET DOMAIN (AGD)-CONTAINING P1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsDu, X. / Du, J.
Funding support China, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology (China)2016YFA0503200 China
CitationJournal: Nat Commun / Year: 2018
Title: Arabidopsis AGDP1 links H3K9me2 to DNA methylation in heterochromatin
Authors: Zhang, C. / Du, X. / Tang, K. / Yang, Z. / Pan, L. / Zhu, P. / Luo, J. / Jiang, Y. / Zhang, H. / Wan, H. / Wang, X. / Wu, F. / Tao, W.A. / He, X.J. / Zhang, H. / Bressan, R.A. / Du, J. / Zhu, J.K.
History
DepositionMay 17, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 14, 2018Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Agenet domain-containing protein


Theoretical massNumber of molelcules
Total (without water)19,3011
Polymers19,3011
Non-polymers00
Water1,56787
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area8540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.177, 57.177, 206.430
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-457-

HOH

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Components

#1: Protein Agenet domain-containing protein / At1g09320


Mass: 19301.209 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: At1g09320, T31J12.4, T31J12_4 / Plasmid: pMBP / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): RIL / References: UniProt: Q500V5
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 87 / 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: 2.54 Å3/Da / Density % sol: 51.61 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 3.5M sodium formate, 0.1M HEPES, pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9778 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 8, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9778 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 14321 / % possible obs: 99.4 % / Redundancy: 15.6 % / Rmerge(I) obs: 0.097 / Net I/σ(I): 56
Reflection shellResolution: 2→2.07 Å / Redundancy: 17.8 % / Rmerge(I) obs: 0.241 / Mean I/σ(I) obs: 17.8 / Num. unique obs: 1369 / % possible all: 98.6

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2→40.192 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 0.77 / Phase error: 21.09
RfactorNum. reflection% reflection
Rfree0.2185 722 5.07 %
Rwork0.1998 --
obs0.2007 14321 99.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2→40.192 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1185 0 0 87 1272
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0041216
X-RAY DIFFRACTIONf_angle_d0.8451644
X-RAY DIFFRACTIONf_dihedral_angle_d14.906449
X-RAY DIFFRACTIONf_chiral_restr0.033167
X-RAY DIFFRACTIONf_plane_restr0.003217
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0001-2.08010.25391440.22912645X-RAY DIFFRACTION98
2.0801-2.17480.21091420.2112673X-RAY DIFFRACTION100
2.1748-2.28950.24541590.22052709X-RAY DIFFRACTION100
2.2895-2.43290.2311850.22322613X-RAY DIFFRACTION100
2.4329-2.62070.25861350.22672708X-RAY DIFFRACTION100
2.6207-2.88440.20721150.25062711X-RAY DIFFRACTION100
2.8844-3.30160.2391580.21752674X-RAY DIFFRACTION100
3.3016-4.15890.22611260.18172698X-RAY DIFFRACTION100
4.1589-40.20.18211240.17362709X-RAY DIFFRACTION100
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)
13.6866-0.2434-0.27252.04190.8142.734-0.2841-0.14810.70090.03750.2739-0.2789-0.25020.118-0.45980.4102-0.0152-0.04350.2919-0.10930.497416.872428.751895.2933
26.6119-1.07922.12723.8251-2.62893.4699-0.09190.55291.4867-0.2720.31061.886-0.4106-1.2277-0.02860.7832-0.0173-0.09540.7590.06211.1176-0.055722.176389.7571
35.28070.2381-1.31383.77440.59884.58190.16850.22470.6067-0.60970.1318-0.5128-0.56890.0946-0.14670.5455-0.03530.10680.3551-0.03240.477615.79623.209486.4066
42.46430.2936-0.60532.58322.24972.417-0.14020.47730.175-0.6296-0.15020.1893-0.4255-0.0982-0.00550.43690.0074-0.02110.3615-0.0470.319511.121818.131684.6617
52.90532.1915-2.42822.013-1.22872.6687-0.4501-1.515-0.96220.46490.0055-0.54540.77210.91990.29750.6590.1740.08910.59080.05260.50948.334511.9292108.8124
63.71210.5255-1.52562.75890.85752.7783-0.19560.097-0.14720.14390.24490.20690.1468-0.04750.23330.34660.01110.01450.2538-0.07330.39010.93469.8676101.8812
74.83620.5241-1.84293.4021-1.06651.92920.0408-0.12350.16320.109-0.09810.4386-0.026-0.04690.14940.43080.0064-0.00230.2794-0.08910.31572.531515.0257102.755
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 206 through 230 )
2X-RAY DIFFRACTION2chain 'A' and (resid 231 through 239 )
3X-RAY DIFFRACTION3chain 'A' and (resid 240 through 258 )
4X-RAY DIFFRACTION4chain 'A' and (resid 259 through 281 )
5X-RAY DIFFRACTION5chain 'A' and (resid 282 through 295 )
6X-RAY DIFFRACTION6chain 'A' and (resid 296 through 317 )
7X-RAY DIFFRACTION7chain 'A' and (resid 318 through 351 )

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