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- PDB-6ie7: Crystal structure of ADCP1 tandem Agenet domain 1-2 in complex wi... -

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Basic information

Entry
Database: PDB / ID: 6ie7
TitleCrystal structure of ADCP1 tandem Agenet domain 1-2 in complex with H3K9me2
Components
  • Agenet domain-containing protein
  • H3K9me2 peptide
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
AMMONIUM ION / Protein AGENET DOMAIN (AGD)-CONTAINING P1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 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

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Assembly

Deposited unit
A: Agenet domain-containing protein
E: H3K9me2 peptide
B: Agenet domain-containing protein
F: H3K9me2 peptide
C: Agenet domain-containing protein
G: H3K9me2 peptide
D: Agenet domain-containing protein
H: H3K9me2 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,12512
Polymers75,0538
Non-polymers724
Water88349
1
A: Agenet domain-containing protein
E: H3K9me2 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,7813
Polymers18,7632
Non-polymers181
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1510 Å2
ΔGint-4 kcal/mol
Surface area8550 Å2
MethodPISA
2
B: Agenet domain-containing protein
F: H3K9me2 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,7813
Polymers18,7632
Non-polymers181
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1510 Å2
ΔGint-2 kcal/mol
Surface area8440 Å2
MethodPISA
3
C: Agenet domain-containing protein
G: H3K9me2 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,7813
Polymers18,7632
Non-polymers181
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1560 Å2
ΔGint-6 kcal/mol
Surface area8400 Å2
MethodPISA
4
D: Agenet domain-containing protein
H: H3K9me2 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,7813
Polymers18,7632
Non-polymers181
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1650 Å2
ΔGint-4 kcal/mol
Surface area8700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.472, 111.338, 68.144
Angle α, β, γ (deg.)90.000, 90.630, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A and segid AA
21chain B and segid BA
31chain C and segid CA
41chain D and segid DA
12chain E and segid E
22chain F and segid F
32chain G and segid G
42chain H and segid H

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain A and segid AAA0
211chain B and segid BAB0
311chain C and segid CAC0
411chain D and segid DAD0
112chain E and segid EE0
212chain F and segid FF0
312chain G and segid GG0
412chain H and segid HH0

NCS ensembles :
ID
1
2

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Components

#1: Protein
Agenet domain-containing protein


Mass: 17484.787 Da / Num. of mol.: 4 / 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
H3K9me2 peptide


Mass: 1278.482 Da / Num. of mol.: 4 / Fragment: H3 peptide 1-15, K9 dimethylation / Source method: obtained synthetically / Details: chemically synthesized H3K9me1 peptide / Source: (synth.) Arabidopsis thaliana (thale cress)
#3: Chemical
ChemComp-NH4 / AMMONIUM ION / Ammonium


Mass: 18.038 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: H4N
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 49 / 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: 2.1 Å3/Da / Density % sol: 41.32 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2M Ammonium acetate, 28% 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: 2.7→50 Å / Num. obs: 15173 / % possible obs: 89.1 % / Redundancy: 2.5 % / Biso Wilson estimate: 44.71 Å2 / Rmerge(I) obs: 0.066 / Rpim(I) all: 0.046 / Rrim(I) all: 0.081 / Χ2: 0.907 / Net I/σ(I): 9 / Num. measured all: 38448
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
HKL-2000data scaling
PHENIX1.9_1692refinement
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→33.908 Å / SU ML: 0.39 / Cross valid method: THROUGHOUT / σ(F): 1.41 / Phase error: 28.67
RfactorNum. reflection% reflection
Rfree0.2556 810 5.35 %
Rwork0.19 --
obs0.1935 15139 88.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 97.78 Å2 / Biso mean: 44.7679 Å2 / Biso min: 16.97 Å2
Refinement stepCycle: final / Resolution: 2.7→33.908 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4658 0 20 49 4727
Biso mean--46.52 36.57 -
Num. residues----568
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0094770
X-RAY DIFFRACTIONf_angle_d1.2586410
X-RAY DIFFRACTIONf_chiral_restr0.051659
X-RAY DIFFRACTIONf_plane_restr0.009809
X-RAY DIFFRACTIONf_dihedral_angle_d14.3451799
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2555X-RAY DIFFRACTION13.489TORSIONAL
12B2555X-RAY DIFFRACTION13.489TORSIONAL
13C2555X-RAY DIFFRACTION13.489TORSIONAL
14D2555X-RAY DIFFRACTION13.489TORSIONAL
21E157X-RAY DIFFRACTION13.489TORSIONAL
22F157X-RAY DIFFRACTION13.489TORSIONAL
23G157X-RAY DIFFRACTION13.489TORSIONAL
24H157X-RAY DIFFRACTION13.489TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.7001-2.86920.34941410.25312420256191
2.8692-3.09060.31441520.23112424257691
3.0906-3.40130.25881370.19542387252489
3.4013-3.89290.26651410.18432292243386
3.8929-4.90230.21351120.15912487259991
4.9023-33.91060.22541270.18982319244685

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