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- PDB-6ie6: Crystal structure of ADCP1 tandem Agenet domain 3-4 in complex wi... -

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Basic information

Entry
Database: PDB / ID: 6ie6
TitleCrystal structure of ADCP1 tandem Agenet domain 3-4 in complex with H3K9me2
Components
  • Agenet domain-containing protein
  • H3K9me2
KeywordsTRANSLATION / Agenet domain
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 / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsZhao, S. / Zhang, B. / Li, H.
CitationJournal: Cell Res. / Year: 2019
Title: ADCP1-tandem Agenet domain 1-2 in complex wit h H3K9me2
Authors: Zhao, S. / Zhang, B. / Li, H.
History
DepositionSep 13, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 16, 2019Provider: 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
P: H3K9me2


Theoretical massNumber of molelcules
Total (without water)19,3442
Polymers19,3442
Non-polymers00
Water3,027168
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1350 Å2
ΔGint-6 kcal/mol
Surface area9130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.891, 56.891, 210.005
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11P-1-

ALA

21A-300-

HOH

31A-314-

HOH

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Components

#1: Protein Agenet domain-containing protein / At1g09320


Mass: 18166.379 Da / Num. of mol.: 1 / Fragment: Agenet domain, UNP residues 201-355
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: ADCP1 / Plasmid: pGEX6p / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q500V5
#2: Protein/peptide H3K9me2 /


Mass: 1177.378 Da / Num. of mol.: 1 / Fragment: H3 peptide 1-15, K9 dimethylation / Source method: obtained synthetically / Details: chemically synthesized H3K9me2 peptide / Source: (synth.) Arabidopsis thaliana (thale cress)
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 168 / 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: 51.5 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.1M HEPES pH 7.5, 2.0M Ammonium formate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 11, 2017 / Details: mirrors
RadiationMonochromator: double crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 22285 / % possible obs: 95.7 % / Redundancy: 5.8 % / Biso Wilson estimate: 30.24 Å2 / Rmerge(I) obs: 0.066 / Rpim(I) all: 0.028 / Rrim(I) all: 0.072 / Χ2: 1.955 / Net I/σ(I): 10.7 / Num. measured all: 129592
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.7-1.736.10.72410960.7930.3090.790.53997
1.73-1.765.90.53211100.8690.2320.5830.52399.2
1.76-1.795.60.43410870.8890.1970.4780.56695.9
1.79-1.836.40.37611060.9430.1570.4090.61997.1
1.83-1.876.60.30710940.9540.1260.3340.71499.1
1.87-1.915.80.30810830.9350.1350.3381.01895.2
1.91-1.965.90.2611030.9530.1120.2851.32796.2
1.96-2.026.20.19511250.9760.0820.2131.15899.4
2.02-2.075.80.19510830.9710.0860.2141.68395.7
2.07-2.145.90.15710860.9840.0670.1711.68994.6
2.14-2.225.80.13411030.9860.0580.1471.81396.5
2.22-2.314.70.139540.9820.0620.1452.4883.1
2.31-2.415.40.1111180.9870.0510.1222.31996.3
2.41-2.544.70.09911250.9910.0480.1112.8597.1
2.54-2.75.60.09411300.990.0420.1042.9696.1
2.7-2.915.90.07911310.9930.0340.0873.30496.1
2.91-3.25.90.06611540.9970.0280.0723.45897.4
3.2-3.6660.05911490.9970.0250.0643.42195.4
3.66-4.615.90.05111410.9980.0210.0553.27492.8
4.61-506.30.05313070.9970.0220.0583.51194.1

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.9_1692refinement
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→31.963 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 22.67 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.232 2217 9.96 %
Rwork0.1862 20051 -
obs0.1906 22268 96.02 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 132.12 Å2 / Biso mean: 48.1525 Å2 / Biso min: 22.27 Å2
Refinement stepCycle: final / Resolution: 1.7→31.963 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1298 0 0 168 1466
Biso mean---53.92 -
Num. residues----160
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071329
X-RAY DIFFRACTIONf_angle_d1.0321790
X-RAY DIFFRACTIONf_chiral_restr0.047185
X-RAY DIFFRACTIONf_plane_restr0.005234
X-RAY DIFFRACTIONf_dihedral_angle_d13.935495
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 16

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7005-1.73750.32541330.25841229136297
1.7375-1.77790.32971420.26121223136596
1.7779-1.82230.27991210.246412741395100
1.8223-1.87160.25851370.22461223136097
1.8716-1.92670.29181530.25831203135696
1.9267-1.98880.26631590.22211215137497
1.9888-2.05990.271630.21131227139097
2.0599-2.14240.24551390.21591214135395
2.1424-2.23990.24761220.19881217133994
2.2399-2.35790.24831250.20341172129790
2.3579-2.50560.25661280.20291256138496
2.5056-2.6990.27581320.20581279141197
2.699-2.97040.24751270.19691289141697
2.9704-3.39980.20881520.17861293144598
3.3998-4.28170.17931250.14841298142393
4.2817-31.96870.22211590.17111439159897
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)
16.83690.3014-1.18182.7754-1.48216.1839-0.3165-0.0092-0.49720.18730.25150.12580.32220.00930.09730.283-0.04370.02130.22690.0530.2759-17.2718-28.8952-8.2083
25.40032.0522-2.75764.59771.40284.4439-0.50171.3264-1.234-1.24640.4601-1.55720.90991.6480.1310.6180.13260.14840.7544-0.01190.5998-1.5603-21.8584-12.8214
38.70353.98830.72292.16780.73058.1148-0.05190.4419-0.4865-0.05090.1027-0.13450.9302-0.13840.02020.4055-0.0189-0.05290.24510.04770.3076-16.5301-23.5001-18.0209
43.29632.1588-1.44917.7673-6.28047.9588-0.12190.3099-0.0845-0.49-0.1264-0.13670.20550.23160.33620.25630.0138-0.01840.2710.03670.2554-11.1123-18.2564-18.8208
56.94557.37186.32628.12116.52265.7563-0.2951-1.3791.6230.5152-0.67520.96-0.0222-1.00310.8810.43880.09740.03780.5657-0.03160.4256-8.6764-11.7065.3601
65.010.1031.89625.24071.71297.6088-0.10370.28890.08770.01590.305-0.175500.3337-0.16830.268-0.0192-0.03180.22970.08220.25181.1-10.7722-1.711
76.61446.96321.41618.91461.63451.02840.246-0.5372-0.36120.3002-0.3531-0.22860.0097-0.12030.10460.3931-0.0113-0.02240.29410.13430.2799-6.1907-16.63390.5544
84.32652.7664.63997.60750.52385.97920.03453.2652-0.3063-0.59570.130.5754-0.7181.92130.03320.74160.1103-0.06191.5040.18420.7929-0.1609-13.0075-18.221
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 11 through 34 )A11 - 34
2X-RAY DIFFRACTION2chain 'A' and (resid 35 through 45 )A35 - 45
3X-RAY DIFFRACTION3chain 'A' and (resid 46 through 63 )A46 - 63
4X-RAY DIFFRACTION4chain 'A' and (resid 64 through 86 )A64 - 86
5X-RAY DIFFRACTION5chain 'A' and (resid 87 through 100 )A87 - 100
6X-RAY DIFFRACTION6chain 'A' and (resid 101 through 132 )A101 - 132
7X-RAY DIFFRACTION7chain 'A' and (resid 133 through 157 )A133 - 157
8X-RAY DIFFRACTION8chain 'P' and (resid 1 through 10 )P1 - 10

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