[English] 日本語
Yorodumi
- PDB-7uw8: Drosophila melanogaster setdb1-tuor domain -

+
Open data


ID or keywords:

Loading...

-
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


: / : / gene silencing by siRNA-directed DNA methylation / : / [histone H3]-lysine9 N-trimethyltransferase / PKMTs methylate histone lysines / female germ-line stem cell asymmetric division / positive regulation of DNA methylation-dependent heterochromatin formation / histone H3K9 methyltransferase activity / polytene chromosome ...: / : / gene silencing by siRNA-directed DNA methylation / : / [histone H3]-lysine9 N-trimethyltransferase / PKMTs methylate histone lysines / female germ-line stem cell asymmetric division / positive regulation of DNA methylation-dependent heterochromatin formation / histone H3K9 methyltransferase activity / polytene chromosome / oogenesis / heterochromatin formation / heterochromatin organization / epigenetic regulation of gene expression / 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)
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more