[English] 日本語
Yorodumi
- PDB-1muh: CRYSTAL STRUCTURE OF TN5 TRANSPOSASE COMPLEXED WITH TRANSPOSON END DNA -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1muh
TitleCRYSTAL STRUCTURE OF TN5 TRANSPOSASE COMPLEXED WITH TRANSPOSON END DNA
Components
  • DNA NON-TRANSFERRED STRAND
  • DNA TRANSFERRED STRAND
  • Tn5 transposase
KeywordsTRANSCRIPTION/DNA / TRANSPOSASE / RIBONUCLEASE H-LIKE MOTIF / PROTEIN-DNA COMPLEX / SYNAPTIC 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 / MAD / Resolution: 2.3 Å
AuthorsThoden, J.B. / Holden, H.M. / Davies, D.R. / Goryshin, I.Y. / Reznikoff, W.S. / Rayment, I.
CitationJournal: Science / Year: 2000
Title: Three-dimensional structure of the Tn5 synaptic complex transposition intermediate.
Authors: Davies, D.R. / Goryshin, I.Y. / Reznikoff, W.S. / Rayment, I.
History
DepositionSep 23, 2002Deposition site: RCSB / Processing site: RCSB
SupersessionSep 27, 2002ID: 1F3I
Revision 1.0Sep 27, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 24, 2019Group: Data collection / Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Oct 27, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / 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_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_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Feb 14, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
B: DNA TRANSFERRED STRAND
C: DNA NON-TRANSFERRED STRAND
A: Tn5 transposase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,1915
Polymers66,1123
Non-polymers792
Water5,513306
1
B: DNA TRANSFERRED STRAND
C: DNA NON-TRANSFERRED STRAND
A: Tn5 transposase
hetero molecules

B: DNA TRANSFERRED STRAND
C: DNA NON-TRANSFERRED STRAND
A: Tn5 transposase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)132,38210
Polymers132,2236
Non-polymers1584
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_554x,x-y,-z-1/61
Unit cell
Length a, b, c (Å)113.700, 113.700, 228.100
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
DetailsHOMODIMER, the second half is generated by: ROTATION MATRIX: 0.50000 0.86603 0.00000 0.86603 -0.50000 0.00000 0.00000 0.00000 -1.00000 TRANSLATION VECTOR IN AS -0.00049 -0.00062 -38.01598

-
Components

-
DNA chain , 2 types, 2 molecules BC

#1: DNA chain DNA TRANSFERRED STRAND


Mass: 6213.039 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: TRANSPOSASE RECOGNITION SEQUENCE OCCURS NATURALLY IN THE TN5 TRANSPOSON
#2: DNA chain DNA NON-TRANSFERRED STRAND


Mass: 6052.943 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: TRANSPOSASE RECOGNITION SEQUENCE OCCURS NATURALLY IN THE TN5 TRANSPOSON

-
Protein , 1 types, 1 molecules A

#3: Protein Tn5 transposase / PLASPOSON PTNMOD-OCM /


Mass: 53845.652 Da / Num. of mol.: 1 / Mutation: E54K, M56A, L372P
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: PTYB1 / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21(de3)pLysS / References: UniProt: Q46731

-
Non-polymers , 3 types, 308 molecules

#4: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 306 / 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: 61.52 %
Crystal growTemperature: 290 K / Method: vapor diffusion / pH: 6
Details: PEG400, Succinate, pH 6.00, VAPOR DIFFUSION, temperature 290K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG40011
2Succinate11
Crystal grow
*PLUS
pH: 7.7 / Method: batch method
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
10.3 M1dropKCl
220 mMHEPES1droppH7.7
32 mMEDTA1drop
410 mg/mlprotein1drop
530 %(w/v)PEG4001reservoir
6100 mMMES1reservoirpH6.0
760 mMammonium sulfate1reservoir

-
Data collection

DiffractionMean temperature: 113 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.70090,0.97910,0.97630, 0.72130
DetectorType: CUSTOM-MADE / Detector: CCD / Date: Dec 17, 1999
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.70091
20.97911
30.97631
40.72131
ReflectionResolution: 2.3→30 Å / Num. obs: 39476 / % possible obs: 99.6 % / Observed criterion σ(I): 0 / Redundancy: 14.94 % / Biso Wilson estimate: 11.3 Å2 / Rmerge(I) obs: 0.053 / Net I/σ(I): 25.56
Reflection
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 30 Å / Redundancy: 14.94 %
Reflection shell
*PLUS
% possible obs: 98.2 % / Rmerge(I) obs: 0.323

-
Processing

Software
NameClassification
TNTrefinement
SCALEPACKdata scaling
CNSrefinement
DENZOdata reduction
CNSphasing
RefinementMethod to determine structure: MAD / Resolution: 2.3→30 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.267 4025 5 %RANDOM
Rwork0.204 ---
all0.206 39412 --
obs0.206 39412 100 %-
Refinement stepCycle: LAST / Resolution: 2.3→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3569 814 2 306 4691
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.015
X-RAY DIFFRACTIONt_angle_deg2.71
Refinement
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 30 Å / Num. reflection obs: 37502 / Num. reflection Rfree: 1974 / % reflection Rfree: 5 % / Rfactor Rfree: 0.257 / Rfactor Rwork: 0.223
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.012
X-RAY DIFFRACTIONt_angle_deg1.795

+
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