[English] 日本語
Yorodumi
- PDB-3m9q: Drosophila MSL3 chromodomain -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3m9q
TitleDrosophila MSL3 chromodomain
ComponentsProtein male-specific lethal-3
KeywordsDNA BINDING PROTEIN / Chromodomain / MSL3 / methyllysine recognition / aromatic cage / MSL complex / transcription upregulation
Function / homology
Function and homology information


: / regulation of hemocyte proliferation / : / : / X chromosome located dosage compensation complex, transcription activating / : / heterochromatin formation => GO:0031507 / HATs acetylate histones / sex-chromosome dosage compensation / : ...: / regulation of hemocyte proliferation / : / : / X chromosome located dosage compensation complex, transcription activating / : / heterochromatin formation => GO:0031507 / HATs acetylate histones / sex-chromosome dosage compensation / : / MSL complex / dosage compensation by hyperactivation of X chromosome / : / chromocenter / polytene chromosome / NuA4 histone acetyltransferase complex / nuclear chromosome / X chromosome / histone acetyltransferase complex / methylated histone binding / mRNA binding / chromatin binding / RNA binding
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #220 / MRG / MRG domain / MRG, C-terminal domain superfamily / MRG / MRG domain profile. / SH3 type barrels. - #140 / Chromo-like domain superfamily / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / SH3 type barrels. ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #220 / MRG / MRG domain / MRG, C-terminal domain superfamily / MRG / MRG domain profile. / SH3 type barrels. - #140 / Chromo-like domain superfamily / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / SH3 type barrels. / Roll / Up-down Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Protein male-specific lethal-3
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.29 Å
AuthorsKim, D. / Huang, P. / Rastinejad, F. / Khorasanizadeh, S.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2010
Title: Corecognition of DNA and a methylated histone tail by the MSL3 chromodomain.
Authors: Kim, D. / Blus, B.J. / Chandra, V. / Huang, P. / Rastinejad, F. / Khorasanizadeh, S.
History
DepositionMar 22, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 21, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Revision 1.3Sep 6, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Protein male-specific lethal-3
B: Protein male-specific lethal-3


Theoretical massNumber of molelcules
Total (without water)24,5622
Polymers24,5622
Non-polymers00
Water9,188510
1
A: Protein male-specific lethal-3


Theoretical massNumber of molelcules
Total (without water)12,2811
Polymers12,2811
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Protein male-specific lethal-3


Theoretical massNumber of molelcules
Total (without water)12,2811
Polymers12,2811
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)60.407, 60.407, 113.805
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-98-

HOH

21A-312-

HOH

-
Components

#1: Protein Protein male-specific lethal-3


Mass: 12281.052 Da / Num. of mol.: 2 / Mutation: C66A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: msl-3, CG8631 / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P50536
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 510 / 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: 2.44 Å3/Da / Density % sol: 49.6 %
Crystal growTemperature: 283 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.2M Sodium acetate, 16% Polyethylene glycol-3350, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 283K

-
Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.29→50 Å / Num. obs: 60843 / % possible obs: 99 % / Redundancy: 8.1 % / Rmerge(I) obs: 0.078 / Χ2: 1.015 / Net I/σ(I): 13.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.29-1.347.20.30157571.01795.4
1.34-1.398.30.23560351.013100
1.39-1.458.40.18360911.009100
1.45-1.538.30.14760741.025100
1.53-1.638.40.12961131.027100
1.63-1.758.50.11661121.016100
1.75-1.937.80.09760471.02398.6
1.93-2.218.20.08661611.037100
2.21-2.787.80.0766098198
2.78-507.70.06363550.98197.9

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.4.0069refinement
PDB_EXTRACT3.005data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2F5K

2f5k


Resolution: 1.29→30.71 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.958 / Occupancy max: 1 / Occupancy min: 0 / SU B: 1.156 / SU ML: 0.028 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.046 / ESU R Free: 0.048 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.192 3087 5.1 %RANDOM
Rwork0.17 ---
obs0.171 60790 99.31 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 83.21 Å2 / Biso mean: 19.151 Å2 / Biso min: 9.24 Å2
Baniso -1Baniso -2Baniso -3
1--0.07 Å2-0.03 Å20 Å2
2---0.07 Å20 Å2
3---0.1 Å2
Refinement stepCycle: LAST / Resolution: 1.29→30.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1468 0 0 510 1978
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0221622
X-RAY DIFFRACTIONr_bond_other_d0.0010.021167
X-RAY DIFFRACTIONr_angle_refined_deg1.1561.9542180
X-RAY DIFFRACTIONr_angle_other_deg1.22332799
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2465195
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.36822.32686
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.13715292
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.351520
X-RAY DIFFRACTIONr_chiral_restr0.0640.2227
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021824
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02370
X-RAY DIFFRACTIONr_mcbond_it0.7522952
X-RAY DIFFRACTIONr_mcbond_other0.1582374
X-RAY DIFFRACTIONr_mcangle_it1.29431540
X-RAY DIFFRACTIONr_scbond_it1.0542670
X-RAY DIFFRACTIONr_scangle_it1.6243640
LS refinement shellResolution: 1.29→1.324 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.255 225 -
Rwork0.217 4144 -
all-4369 -
obs--98.14 %
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)
10.28970.01410.15780.7091-0.49390.94870.0030.01910.03620.02220.00940.0068-0.0945-0.0109-0.0124-0.08560.00010.0001-0.1039-0.0044-0.1358-27.35422.665-5.6
20.7678-0.5807-0.54650.95320.42280.8995-0.03430.0237-0.1167-0.0006-0.01750.18680.0632-0.09030.0519-0.07460.007-0.0024-0.0811-0.0037-0.097-44.7615.24215.955
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A7 - 90
2X-RAY DIFFRACTION2B7 - 90

+
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://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