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- PDB-7uve: Drosophila melanogaster setdb1-tuor domain with peptide H3K9me2K14ac -

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Basic information

Entry
Database: PDB / ID: 7uve
TitleDrosophila melanogaster setdb1-tuor domain with peptide H3K9me2K14ac
Components
  • Histone-lysine N-methyltransferase eggless
  • peptide H3K9me2K14ac
KeywordsTRANSFERASE / setdb1-tuor domain / H3K9me2K14ac / Structural Genomics / Structural Genomics Consortium / SGC / PSI-2 / Protein Structure Initiative
Function / homology
Function and homology information


: / : / : / [histone H3]-lysine9 N-trimethyltransferase / PKMTs methylate histone lysines / gene silencing by siRNA-directed DNA methylation / female germ-line stem cell asymmetric division / positive regulation of DNA methylation-dependent heterochromatin formation / polytene chromosome / heterochromatin organization ...: / : / : / [histone H3]-lysine9 N-trimethyltransferase / PKMTs methylate histone lysines / gene silencing by siRNA-directed DNA methylation / female germ-line stem cell asymmetric division / positive regulation of DNA methylation-dependent heterochromatin formation / polytene chromosome / heterochromatin organization / histone H3K9 methyltransferase activity / oogenesis / epigenetic regulation of gene expression / heterochromatin formation / negative regulation of gene expression / DNA binding / zinc ion binding / nucleus / cytoplasm
Similarity search - Function
Histone methyltransferase, Tudor domain 1 / Histone methyltransferase, Tudor domain 2 / Histone methyltransferase Tudor domain / Histone methyltransferase Tudor domain 1 / Pre-SET domain / Pre-SET motif / Pre-SET domain profile. / N-terminal to some SET domains / Post-SET domain / Post-SET domain profile. ...Histone methyltransferase, Tudor domain 1 / Histone methyltransferase, Tudor domain 2 / Histone methyltransferase Tudor domain / Histone methyltransferase Tudor domain 1 / Pre-SET domain / Pre-SET motif / Pre-SET domain profile. / N-terminal to some SET domains / Post-SET domain / Post-SET domain profile. / Methyl-CpG binding domain / Methyl-CpG DNA binding / Methyl-CpG binding domain / Methyl-CpG-binding domain (MBD) profile. / DNA-binding domain superfamily / SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain / SET domain superfamily / SET domain / SET domain profile. / SET domain
Similarity search - Domain/homology
Histone-lysine N-methyltransferase eggless
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
Drosophila sechellia (fry)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.3 Å
AuthorsZhou, M. / Dong, A. / Liu, K. / Arrowsmith, C.H. / Edwards, A.M. / Min, J. / Structural Genomics Consortium (SGC)
Funding support1items
OrganizationGrant numberCountry
Other private
CitationJournal: To Be Published
Title: Drosophila melanogaster setdb1-tuor domain with peptide H3K9me2K14ac
Authors: Zhou, M. / Dong, A. / Liu, K. / Arrowsmith, C.H. / Edwards, A.M. / Min, J. / Structural Genomics Consortium (SGC)
History
DepositionMay 1, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 10, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Histone-lysine N-methyltransferase eggless
B: peptide H3K9me2K14ac


Theoretical massNumber of molelcules
Total (without water)31,4542
Polymers31,4542
Non-polymers00
Water52229
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1020 Å2
ΔGint-6 kcal/mol
Surface area12610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.269, 111.134, 112.149
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222

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Components

#1: Protein Histone-lysine N-methyltransferase eggless / SETDB1 homolog


Mass: 29550.613 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: egg, CG12196 / Plasmid: pET28-MKH8SUMO / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): -V2R-pRARE2
References: UniProt: Q32KD2, [histone H3]-lysine9 N-trimethyltransferase
#2: Protein/peptide peptide H3K9me2K14ac


Mass: 1903.191 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Drosophila sechellia (fry)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 29 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 3.02 Å3/Da / Density % sol: 59.3 % / Mosaicity: 1.266 °
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 15% PEG 8000, 0.2M Magnesium Chloride,0.1M tris pH8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E / Wavelength: 1.54178 Å
DetectorType: RIGAKU SATURN A200 / Detector: CCD / Date: May 23, 2019
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 16672 / % possible obs: 96.1 % / Redundancy: 12.1 % / Biso Wilson estimate: 51.49 Å2 / Rmerge(I) obs: 0.096 / Rpim(I) all: 0.028 / Rrim(I) all: 0.1 / Χ2: 1.824 / Net I/σ(I): 11.6 / Num. measured all: 202427
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.3-2.348.60.886220.9030.2950.9321.19572.7
2.34-2.389.10.7756800.9230.2520.8181.06280
2.38-2.439.90.817370.9430.2560.8521.13185.3
2.43-2.4810.50.8227730.930.2520.8621.12990.5
2.48-2.5311.10.8148000.9510.2450.8521.08494.6
2.53-2.59120.6278470.9750.1850.6551.06498.3
2.59-2.6612.50.6288500.9770.1820.6541.16599.9
2.66-2.7313.10.5248630.9750.1490.5451.268100
2.73-2.8113.30.4538590.9850.1280.4711.358100
2.81-2.913.20.3238520.9890.0920.3361.396100
2.9-313.40.2458630.9910.0690.2551.56100
3-3.1213.30.1848630.9950.0520.1911.6299.9
3.12-3.2613.30.1448680.9970.0410.151.734100
3.26-3.4413.10.1358560.9980.0390.142.393100
3.44-3.6512.10.1088660.9970.0320.1133.69199.9
3.65-3.9312.10.0778610.9980.0230.0813.347100
3.93-4.3312.40.0568880.9990.0160.0582.71799.9
4.33-4.9512.90.04388610.0120.0452.372100
4.95-6.24130.04389110.0120.0452100
6.24-5011.70.03494710.010.0352.05599.2

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation4.55 Å31.91 Å
Translation4.55 Å31.91 Å

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
HKL-2000data scaling
PHASER2.8.2phasing
PDB_EXTRACT3.27data extraction
HKL-3000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6BHH

6bhh


Resolution: 2.3→21.06 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.906 / SU R Cruickshank DPI: 0.265 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.26 / SU Rfree Blow DPI: 0.225 / SU Rfree Cruickshank DPI: 0.229
RfactorNum. reflection% reflectionSelection details
Rfree0.289 843 5.13 %RANDOM
Rwork0.246 ---
obs0.249 16432 94.7 %-
Displacement parametersBiso max: 126.47 Å2 / Biso mean: 60.04 Å2 / Biso min: 27.7 Å2
Baniso -1Baniso -2Baniso -3
1--10.2665 Å20 Å20 Å2
2--9.2427 Å20 Å2
3---1.0237 Å2
Refine analyzeLuzzati coordinate error obs: 0.39 Å
Refinement stepCycle: final / Resolution: 2.3→21.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1846 0 0 29 1875
Biso mean---49.53 -
Num. residues----236
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d621SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes320HARMONIC5
X-RAY DIFFRACTIONt_it1906HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion256SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact2132SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d1906HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg2602HARMONIC21.08
X-RAY DIFFRACTIONt_omega_torsion3.33
X-RAY DIFFRACTIONt_other_torsion16.66
LS refinement shellResolution: 2.3→2.33 Å / Rfactor Rfree error: 0 / Total num. of bins used: 42
RfactorNum. reflection% reflection
Rfree0.3511 25 6.38 %
Rwork0.3262 367 -
all0.3282 392 -
obs--69.38 %
Refinement TLS params.Method: refined / Origin x: 35.0391 Å / Origin y: 29.7493 Å / Origin z: 15.2446 Å
111213212223313233
T0.2578 Å2-0.0456 Å2-0.036 Å2--0.2245 Å20.0524 Å2---0.2245 Å2
L1.1597 °2-0.6021 °2-0.1154 °2-2.2332 °20.6001 °2--1.3895 °2
S0.1234 Å °-0.1467 Å °-0.0808 Å °0.3949 Å °-0.0826 Å °-0.076 Å °0.0679 Å °0.1804 Å °-0.0408 Å °
Refinement TLS groupSelection details: { A|* }

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