[English] 日本語
Yorodumi
- PDB-1mm8: Crystal structure of Tn5 Transposase complexed with ME DNA -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1mm8
TitleCrystal structure of Tn5 Transposase complexed with ME DNA
Components
  • ME DNA non-transferred strand
  • ME DNA transferred strand
  • Tn5 Transposase
KeywordsTRANSCRIPTION/DNA / protein-DNA complex / TRANSCRIPTION-DNA COMPLEX
Function / homology
Function and homology information


transposase activity / DNA transposition / endonuclease activity / Hydrolases; Acting on ester bonds / DNA binding / metal ion binding
Similarity search - Function
Tn5 transposase; domain 1 / Transferase Inhibitor Protein From Tn5; Chain A, domain2 / Transferase Inhibitor Protein From Tn5; Chain / Transposase Inhibitor Protein From Tn5; Chain A, domain 1 / Transposase Inhibitor Protein From Tn5; Chain A, domain 1 / Transposase, IS4-like / Transposase, Tn5-like, N-terminal / Transposase, Tn5-like, C-terminal / Transposase, Tn5-like, N-terminal domain superfamily / : ...Tn5 transposase; domain 1 / Transferase Inhibitor Protein From Tn5; Chain A, domain2 / Transferase Inhibitor Protein From Tn5; Chain / Transposase Inhibitor Protein From Tn5; Chain A, domain 1 / Transposase Inhibitor Protein From Tn5; Chain A, domain 1 / Transposase, IS4-like / Transposase, Tn5-like, N-terminal / Transposase, Tn5-like, C-terminal / Transposase, Tn5-like, N-terminal domain superfamily / : / Transposase DDE domain / Transposase DNA-binding / Serum Albumin; Chain A, Domain 1 / Ribonuclease H-like superfamily / Alpha-Beta Complex / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
: / DNA / DNA (> 10) / Transposase for transposon Tn5
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsSteiniger-White, M. / Bhasin, A. / Lovell, S. / Rayment, I. / Reznikoff, W.S.
CitationJournal: J.Mol.Biol. / Year: 2002
Title: Evidence for "unseen" Transposase--DNA contacts
Authors: Steiniger-White, M. / Bhasin, A. / Lovell, S. / Rayment, I. / Reznikoff, W.S.
History
DepositionSep 3, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 13, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref / 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_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_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.pdbx_seq_one_letter_code / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Feb 14, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
B: ME DNA transferred strand
C: ME DNA non-transferred strand
A: Tn5 Transposase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,2225
Polymers66,1123
Non-polymers1102
Water4,576254
1
B: ME DNA transferred strand
C: ME DNA non-transferred strand
A: Tn5 Transposase
hetero molecules

B: ME DNA transferred strand
C: ME DNA non-transferred strand
A: Tn5 Transposase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)132,44310
Polymers132,2236
Non-polymers2204
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_566x,x-y+1,-z+11/61
Unit cell
Length a, b, c (Å)112.500, 112.500, 233.500
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

-
Components

#1: DNA chain ME DNA transferred strand


Mass: 6271.091 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: DNA synthesized by IDT
#2: DNA chain ME DNA non-transferred strand


Mass: 5994.890 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: DNA synthesized by IDT
#3: Protein Tn5 Transposase


Mass: 53845.719 Da / Num. of mol.: 1 / Mutation: E58K, M60A, E349K, L376P
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: Tn5 Transposases / Plasmid: pTYB4 / Production host: Escherichia coli (E. coli) / Strain (production host): ER2566 / References: UniProt: Q46731
#4: Chemical ChemComp-MN / MANGANESE (II) ION


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


Mass: 18.015 Da / Num. of mol.: 254 / 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: 3.2 Å3/Da / Density % sol: 61.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 15% Peg 1500, 300 mM Na tartrate, 50 mM Hepes, 5 mM MnCl2, pH 8., VAPOR DIFFUSION, HANGING DROP, temperature 293K
Components of the solutions
IDNameCrystal-IDSol-ID
1Peg 150011
2Na tartrate11
3Hepes11
4MnCl211
5Na tartrate12
6MnCl212
Crystal grow
*PLUS
pH: 7.7
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
1300 mM1dropKCl
220 mMHEPES1droppH7.7
32 mMEDTA1drop
410 mg/mlprotein1drop
515 %(w/v)PEG15001reservoir
6300 mMsodium tartrate1reservoir
750 mMHEPES1reservoirpH8.0

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.96486 Å
DetectorType: CUSTOM-MADE / Detector: CCD / Date: Mar 22, 2001
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96486 Å / Relative weight: 1
ReflectionResolution: 2.8→500 Å / Num. all: 22984 / Num. obs: 22984 / % possible obs: 90 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.145
Reflection shellResolution: 1.9→2.8 Å / % possible all: 50
Reflection
*PLUS
Highest resolution: 2.9 Å / Lowest resolution: 500 Å / % possible obs: 90 % / Num. measured all: 299225

-
Processing

Software
NameClassification
HKL-2000data collection
SCALEPACKdata scaling
EPMRphasing
CNSrefinement
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→500 Å / Isotropic thermal model: isotropic / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.271 1034 random
Rwork0.217 --
all-22984 -
obs-22984 -
Refinement stepCycle: LAST / Resolution: 2.8→500 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3563 814 2 254 4633
Refinement
*PLUS
Highest resolution: 2.9 Å / Lowest resolution: 500 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS

+
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