[English] 日本語
Yorodumi
- PDB-4r79: Mos1 transposase paired-end complex with left transposon end -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4r79
TitleMos1 transposase paired-end complex with left transposon end
Components
  • (left Inverted repeat ...) x 3
  • Mariner Mos1 transposase
KeywordsRecombination/DNA / transposase / protein-DNA complex / transpososome / Rnase-H like catalytic fold Helix-turn-helix / DNA transposition / DNA cleavage / DNA integration / transposon / inverted repeats / Recombination-DNA complex
Function / homology
Function and homology information


DNA integration / endonuclease activity / DNA recombination / Hydrolases; Acting on ester bonds / DNA binding / metal ion binding / nucleus
Similarity search - Function
Arc Repressor Mutant, subunit A - #1450 / Transposase, type 1 / Mos1 transposase, HTH domain / Transposase (partial DDE domain) / HTH domain in Mos1 transposase / Ribonuclease H-like superfamily/Ribonuclease H / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Nucleotidyltransferase; domain 5 / Arc Repressor Mutant, subunit A / Ribonuclease H superfamily ...Arc Repressor Mutant, subunit A - #1450 / Transposase, type 1 / Mos1 transposase, HTH domain / Transposase (partial DDE domain) / HTH domain in Mos1 transposase / Ribonuclease H-like superfamily/Ribonuclease H / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Nucleotidyltransferase; domain 5 / Arc Repressor Mutant, subunit A / Ribonuclease H superfamily / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
: / DNA / DNA (> 10) / Mariner Mos1 transposase
Similarity search - Component
Biological speciesDrosophila mauritiana (fry)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.1 Å
AuthorsRichardson, J.M.
CitationJournal: J.Biol.Chem. / Year: 2015
Title: Structural Basis for the Inverted Repeat Preferences of mariner Transposases.
Authors: Trubitsyna, M. / Grey, H. / Houston, D.R. / Finnegan, D.J. / Richardson, J.M.
History
DepositionAug 27, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 22, 2015Provider: repository / Type: Initial release
Revision 1.1Jun 10, 2015Group: Database references
Revision 1.2Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
C: left Inverted repeat NTS
D: left Inverted repeat TS
E: left Inverted repeat NTS
F: left Inverted repeat TS
G: left Inverted repeat NTS
H: left Inverted repeat NTS H
A: Mariner Mos1 transposase
B: Mariner Mos1 transposase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)130,66212
Polymers130,3608
Non-polymers3024
Water905
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)119.783, 86.885, 132.379
Angle α, β, γ (deg.)90.00, 99.03, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12C
22E
13D
23F

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1112A4 - 345
2112B4 - 345
1121C4 - 28
2121E4 - 28
1131D29 - 56
2131F29 - 56

NCS ensembles :
ID
1
2
3
Detailsbiological unit is the same as asym.

-
Components

-
Left Inverted repeat ... , 3 types, 6 molecules CEGDFH

#1: DNA chain left Inverted repeat NTS


Mass: 7834.055 Da / Num. of mol.: 3 / Source method: obtained synthetically / Details: Synthesised by IDT / Source: (synth.) synthetic construct (others)
#2: DNA chain left Inverted repeat TS


Mass: 8485.480 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Synthesised by IDT / Source: (synth.) synthetic construct (others)
#3: DNA chain left Inverted repeat NTS H


Mass: 8156.274 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Synthesised by IDT / Source: (synth.) synthetic construct (others)

-
Protein , 1 types, 2 molecules AB

#4: Protein Mariner Mos1 transposase / Transposable element Mos1 transposase


Mass: 40865.316 Da / Num. of mol.: 2 / Mutation: T216A, K243R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila mauritiana (fry) / Gene: mariner\T, T / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q7JQ07, Hydrolases; Acting on ester bonds

-
Non-polymers , 3 types, 9 molecules

#5: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: H2O

-
Details

Sequence detailsAUTHOR STATES THAT ENTRY SEQUENCE OF 4R79 IS CORRECT FOR MOS1. THE REFERENCE J7JQ07 ACTUALLY REFERS ...AUTHOR STATES THAT ENTRY SEQUENCE OF 4R79 IS CORRECT FOR MOS1. THE REFERENCE J7JQ07 ACTUALLY REFERS TO THE PEACH ELEMENT RATHER THAN MOS1. THE ENTRY SEQUENCE HAS 4 DIFFERENCES AGAINST J7JQ07, AS INDICATED IN FIGURE 2 OF THE PAPER BY MEDHORA ET AL IN GENETICS 128:311-318 JUNE,1991. PMCID:PMC1204469. THESE 4 DIFFERENCES SEEM TO MATCH WITH THE VARIANTS HIGHLIGHTED.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 5.22 Å3/Da / Density % sol: 76.43 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 5.8
Details: 100 mM Sodium Citrate pH 5.8, 100 mM Ammonium Acetate, 450 mM KCl, and 5 mM MnCl2, hanging drop, temperature 290K, VAPOR DIFFUSION, HANGING DROP

-
Data collection

DiffractionMean temperature: 70 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.9765 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 10, 2010
RadiationMonochromator: Si 111 channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9765 Å / Relative weight: 1
ReflectionResolution: 3.1→30 Å / Num. all: 48795 / Num. obs: 48795 / % possible obs: 99.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5 % / Rmerge(I) obs: 0.154 / Net I/σ(I): 9.9
Reflection shellResolution: 3.1→3.27 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.359 / Mean I/σ(I) obs: 2.3 / % possible all: 99.1

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALEPACKdata scaling
PHASERphasing
DMphasing
REFMAC5.7.0032refinement
PDB_EXTRACT3.15data extraction
ADSCQuantumdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3HOS

3hos


Resolution: 3.1→29.87 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.904 / SU B: 21.722 / SU ML: 0.352 / Cross valid method: THROUGHOUT / ESU R: 0.646 / ESU R Free: 0.373 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.27009 2444 5 %RANDOM
Rwork0.22719 ---
obs0.22937 46335 99.4 %-
all-48795 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 75.457 Å2
Baniso -1Baniso -2Baniso -3
1-4.81 Å20 Å2-5.48 Å2
2--7.36 Å20 Å2
3----9.93 Å2
Refinement stepCycle: LAST / Resolution: 3.1→29.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5606 3230 12 5 8853
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0169382
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.8511.6213360
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8785668
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.77623.355310
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.903151030
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.2291554
X-RAY DIFFRACTIONr_chiral_restr0.0730.21268
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0216123
X-RAY DIFFRACTIONr_gen_planes_other0.0050.022214
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it5.8176.8712684
X-RAY DIFFRACTIONr_mcbond_other10.3226.4122691
X-RAY DIFFRACTIONr_mcangle_it9.37610.2843348
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it7.6767.7736698
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A3526MEDIUM POSITIONAL0.080.5
1A1986TIGHT THERMAL7.370.5
1A3526MEDIUM THERMAL8.712
2C707TIGHT THERMAL6.470.5
3D878TIGHT THERMAL6.70.5
LS refinement shellResolution: 3.1→3.18 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.394 157 -
Rwork0.411 3314 -
obs--98.8 %

+
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