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- PDB-6ie4: Crystal structure of ADCP1 tandem Agenet domain 1-2 in complex wi... -

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Basic information

Entry
Database: PDB / ID: 6ie4
TitleCrystal structure of ADCP1 tandem Agenet domain 1-2 in complex with H3K9me1
Components
  • Agenet domain-containing protein
  • H3K9me1 peptide
KeywordsTRANSLATION / Agenet domain
Function / homology
Function and homology information


DNA methylation-dependent constitutive heterochromatin formation / : / histone reader activity / chromosome, centromeric region / heterochromatin / 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: 2.696 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
Revision 1.1Apr 9, 2025Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Agenet domain-containing protein
B: H3K9me1 peptide
C: Agenet domain-containing protein
D: H3K9me1 peptide


Theoretical massNumber of molelcules
Total (without water)37,4984
Polymers37,4984
Non-polymers00
Water64936
1
A: Agenet domain-containing protein
B: H3K9me1 peptide


Theoretical massNumber of molelcules
Total (without water)18,7492
Polymers18,7492
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1430 Å2
ΔGint-5 kcal/mol
Surface area8690 Å2
MethodPISA
2
C: Agenet domain-containing protein
D: H3K9me1 peptide


Theoretical massNumber of molelcules
Total (without water)18,7492
Polymers18,7492
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1390 Å2
ΔGint-5 kcal/mol
Surface area8660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.515, 67.529, 116.679
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Agenet domain-containing protein / At1g09320


Mass: 17484.787 Da / Num. of mol.: 2 / Fragment: Agenet domain, UNP residues 31-177
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 H3K9me1 peptide


Mass: 1264.455 Da / Num. of mol.: 2 / Fragment: H3 peptide 1-15, K9 dimethylation / Source method: obtained synthetically / Details: chemically synthesized H3K9me1 peptide / Source: (synth.) Arabidopsis thaliana (thale cress)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 36 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.28 Å3/Da / Density % sol: 46.13 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2M Ammonium acetate, 30% PEG 4000, 0.1M Sodium acetate pH 5.0

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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: 2.696→50 Å / Num. obs: 9743 / % possible obs: 89.1 % / Redundancy: 2.5 % / Rmerge(I) obs: 0.066 / Rpim(I) all: 0.046 / Rrim(I) all: 0.081 / Χ2: 0.907 / Net I/σ(I): 9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.7-2.752.50.2958080.8950.2090.3630.48291.9
2.75-2.82.60.267420.9250.1830.320.45892.1
2.8-2.852.50.2437940.9060.1730.30.52692.1
2.85-2.912.50.2097830.9320.1480.2580.52492.2
2.91-2.972.50.1767870.950.1250.2170.52491.2
2.97-3.042.60.1497490.9720.1060.1830.5491.5
3.04-3.122.50.127690.9830.0850.1480.52691.2
3.12-3.22.50.1137660.9770.0820.1410.67788.5
3.2-3.32.50.0957470.9840.0670.1170.82390.1
3.3-3.42.50.0757520.9910.0520.0910.78388
3.4-3.522.50.0767420.9920.0550.0940.94987.1
3.52-3.662.30.0666700.9940.050.0831.06680.7
3.66-3.832.50.0687750.9920.0480.0841.04588.8
3.83-4.032.60.067670.9940.0410.0731.11992.4
4.03-4.292.60.0527920.9940.0360.0631.3291.6
4.29-4.622.60.0497720.9950.0340.061.50390.1
4.62-5.082.60.0497660.9920.0340.061.30290.9
5.08-5.812.60.057540.9930.0350.0621.06488.3
5.81-7.322.50.0456820.9950.0340.0571.22879
7.32-502.70.047560.9960.0280.0491.61785.5

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Processing

Software
NameVersionClassification
PHENIX(1.14rc3_3206: ???)refinement
HKL-2000data scaling
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.696→44.147 Å / SU ML: 0.38 / Cross valid method: THROUGHOUT / σ(F): 1.4 / Phase error: 26.36
RfactorNum. reflection% reflection
Rfree0.2689 991 10.17 %
Rwork0.2015 --
obs0.2084 9743 99.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.696→44.147 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2395 0 0 36 2431
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092452
X-RAY DIFFRACTIONf_angle_d1.1363295
X-RAY DIFFRACTIONf_dihedral_angle_d20.1571472
X-RAY DIFFRACTIONf_chiral_restr0.066341
X-RAY DIFFRACTIONf_plane_restr0.01417
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6957-2.83780.37181380.27641213X-RAY DIFFRACTION99
2.8378-3.01550.33051300.24491215X-RAY DIFFRACTION99
3.0155-3.24830.31751640.22651207X-RAY DIFFRACTION100
3.2483-3.57510.29411370.20691241X-RAY DIFFRACTION100
3.5751-4.09210.25191260.18861255X-RAY DIFFRACTION100
4.0921-5.15430.23191380.16571285X-RAY DIFFRACTION100
5.1543-44.15240.2351580.20341336X-RAY DIFFRACTION100

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