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- PDB-7uw8: Drosophila melanogaster setdb1-tuor domain -

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Basic information

Entry
Database: PDB / ID: 7uw8
TitleDrosophila melanogaster setdb1-tuor domain
ComponentsHistone-lysine N-methyltransferase eggless
KeywordsTRANSFERASE / setdb1-tuor domain / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


[histone H3]-lysine9 N-trimethyltransferase / PKMTs methylate histone lysines / Regulation of endogenous retroelements by KRAB-ZFP proteins / histone H3K9 trimethyltransferase activity / female germ-line stem cell asymmetric division / transposable element silencing by heterochromatin formation / transposable element silencing by piRNA-mediated heterochromatin formation / : / polytene chromosome / heterochromatin organization ...[histone H3]-lysine9 N-trimethyltransferase / PKMTs methylate histone lysines / Regulation of endogenous retroelements by KRAB-ZFP proteins / histone H3K9 trimethyltransferase activity / female germ-line stem cell asymmetric division / transposable element silencing by heterochromatin formation / transposable element silencing by piRNA-mediated heterochromatin formation / : / polytene chromosome / heterochromatin organization / histone H3K9 methyltransferase activity / histone H3K9me2 methyltransferase activity / oogenesis / epigenetic regulation of gene expression / heterochromatin formation / methylation / 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 motif / Pre-SET domain / Pre-SET domain profile. / N-terminal to some SET domains ...Histone methyltransferase, Tudor domain 1 / Histone methyltransferase, Tudor domain 2 / Histone methyltransferase Tudor domain / Histone methyltransferase Tudor domain 1 / : / : / Pre-SET motif / Pre-SET domain / 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 / SET domain superfamily / SET domain profile. / SET domain
Similarity search - Domain/homology
Histone-lysine N-methyltransferase eggless
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 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
Authors: Zhou, M. / Dong, A. / Liu, K. / Arrowsmith, C.H. / Edwards, A.M. / Min, J. / Structural Genomics Consortium (SGC)
History
DepositionMay 3, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Histone-lysine N-methyltransferase eggless


Theoretical massNumber of molelcules
Total (without water)29,5511
Polymers29,5511
Non-polymers00
Water27015
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)59.989, 110.673, 115.313
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 15 / 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: 3.24 Å3/Da / Density % sol: 62.02 % / Mosaicity: 0.34 °
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 1.6M ammonium sulphate, 0.01M 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: Apr 3, 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: 2.5→39.92 Å / Num. obs: 13531 / % possible obs: 99.4 % / Redundancy: 7.1 % / Biso Wilson estimate: 66.26 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.08 / Rpim(I) all: 0.032 / Rrim(I) all: 0.086 / Net I/σ(I): 21.7 / Num. measured all: 96242 / Scaling rejects: 10
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.5-2.67.11.3691034414510.8590.5411.4741.997
9.01-39.926.10.01920333310.9990.0080.02183.598.2

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.7.4data scaling
BUSTER2.10.3refinement
PDB_EXTRACT3.27data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6BHD

6bhd


Resolution: 2.5→38.91 Å / Cor.coef. Fo:Fc: 0.912 / Cor.coef. Fo:Fc free: 0.912 / SU R Cruickshank DPI: 0.307 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.301 / SU Rfree Blow DPI: 0.244 / SU Rfree Cruickshank DPI: 0.248
RfactorNum. reflection% reflectionSelection details
Rfree0.276 629 4.65 %RANDOM
Rwork0.237 ---
obs0.238 13521 99.1 %-
Displacement parametersBiso max: 138.51 Å2 / Biso mean: 66.13 Å2 / Biso min: 40.92 Å2
Baniso -1Baniso -2Baniso -3
1--18.2775 Å20 Å20 Å2
2--14.6282 Å20 Å2
3---3.6493 Å2
Refine analyzeLuzzati coordinate error obs: 0.42 Å
Refinement stepCycle: final / Resolution: 2.5→38.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1732 0 0 15 1747
Biso mean---55.23 -
Num. residues----221
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d569SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes294HARMONIC5
X-RAY DIFFRACTIONt_it1777HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion241SEMIHARMONIC5
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_contact1961SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d1777HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg2427HARMONIC21.1
X-RAY DIFFRACTIONt_omega_torsion3.18
X-RAY DIFFRACTIONt_other_torsion18.7
LS refinement shellResolution: 2.5→2.53 Å / Rfactor Rfree error: 0 / Total num. of bins used: 31
RfactorNum. reflection% reflection
Rfree0.3335 20 4.58 %
Rwork0.2664 417 -
all0.2695 437 -
obs--90.76 %
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)
11.9568-1.97170.3962.4419-1.59473.76350.03730.0025-0.064-0.04240.007-0.03250.09230.0597-0.04430.19450.0082-0.0371-0.26090.0731-0.029539.157519.55448.1537
20.33052.39552.47293.61231.52173.7972-0.0373-0.1837-0.2110.1439-0.19540.13290.08090.16340.23280.23160.0757-0.0362-0.31090.10490.053336.48178.306814.7624
33.6469-1.4982-0.95296.62370.95453.12490.0799-0.0270.05340.1812-0.1608-0.1589-0.24520.23740.08090.2056-0.0109-0.1016-0.20860.0499-0.156637.924430.454910.733
40.9498-0.2207-0.83163.97561.79523.0915-0.0571-0.0291-0.12230.176-0.09320.072-0.0563-0.09650.15030.1947-0.00010.0014-0.26060.007-0.050925.963839.929218.2098
52.9056-1.963-3.0490.9084-0.69647.7156-0.0123-0.0424-0.30430.2980.0916-0.17070.00610.0921-0.07940.3101-0.0268-0.0535-0.31780.0232-0.090330.609545.550424.7875
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|449 - A|477 }A449 - 477
2X-RAY DIFFRACTION2{ A|478 - A|519 }A478 - 519
3X-RAY DIFFRACTION3{ A|520 - A|601 }A520 - 601
4X-RAY DIFFRACTION4{ A|602 - A|642 }A602 - 642
5X-RAY DIFFRACTION5{ A|643 - A|689 }A643 - 689

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