[English] 日本語
Yorodumi
- PDB-2xo6: DEINOCOCCUS RADIODURANS ISDRA2 TRANSPOSASE Y132F MUTANT COMPLEXED... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2xo6
TitleDEINOCOCCUS RADIODURANS ISDRA2 TRANSPOSASE Y132F MUTANT COMPLEXED WITH LEFT END RECOGNITION AND CLEAVAGE SITE
Components
  • 5'-D(*TP*TP*GP*AP*TP*G)-3'
  • DRA2 TRANSPOSASE LEFT END RECOGNITION SEQUENCE
  • TRANSPOSASE
KeywordsDNA BINDING PROTEIN/DNA / DNA BINDING PROTEIN-DNA COMPLEX / TRANSPOSITION / MOBILE ELEMENT
Function / homology
Function and homology information


transposase activity / DNA transposition / endonuclease activity / DNA binding / metal ion binding
Similarity search - Function
Transposase IS200 like / Transposase IS200-like / Transposase IS200-like / Transposase IS200-like superfamily / Transposase IS200 like / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / : / DNA / DNA (> 10) / ISDra2 transposase TnpA
Similarity search - Component
Biological speciesDEINOCOCCUS RADIODURANS (radioresistant)
SYNTHETIC CONSTRUCT (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsHickman, A.B. / James, J.A. / Barabas, O. / Pasternak, C. / Ton-Hoang, B. / Chandler, M. / Sommer, S. / Dyda, F.
CitationJournal: Embo J. / Year: 2010
Title: DNA Recognition and the Precleavage State During Single-Stranded DNA Transposition in D. Radiodurans.
Authors: Hickman, A.B. / James, J.A. / Barabas, O. / Pasternak, C. / Ton-Hoang, B. / Chandler, M. / Sommer, S. / Dyda, F.
History
DepositionAug 9, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 13, 2010Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc ...exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / pdbx_seq_map_depositor_info
Item: _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval / _pdbx_seq_map_depositor_info.one_letter_code_mod
Revision 1.4Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_alt_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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.ptnr1_symmetry / _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_conn.ptnr2_symmetry / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: TRANSPOSASE
B: DRA2 TRANSPOSASE LEFT END RECOGNITION SEQUENCE
C: 5'-D(*TP*TP*GP*AP*TP*G)-3'
D: TRANSPOSASE
E: DRA2 TRANSPOSASE LEFT END RECOGNITION SEQUENCE
F: 5'-D(*TP*TP*GP*AP*TP*G)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,68824
Polymers52,4236
Non-polymers1,26518
Water7,260403
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18650 Å2
ΔGint-154.6 kcal/mol
Surface area16960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.308, 86.915, 128.297
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

-
Protein , 1 types, 2 molecules AD

#1: Protein TRANSPOSASE / DRA2 TRANSPOSASE


Mass: 16119.772 Da / Num. of mol.: 2 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) DEINOCOCCUS RADIODURANS (radioresistant)
Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O83028

-
DNA chain , 2 types, 4 molecules BECF

#2: DNA chain DRA2 TRANSPOSASE LEFT END RECOGNITION SEQUENCE


Mass: 8252.322 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others)
#3: DNA chain 5'-D(*TP*TP*GP*AP*TP*G)-3' / DRA2 TRANSPOSASE LEFT END CLEAVAGE SITE


Mass: 1839.239 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: DRA2 TRANSPOSON INTERNAL SEQUENCE / Source: (synth.) SYNTHETIC CONSTRUCT (others)

-
Non-polymers , 4 types, 421 molecules

#4: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Cd
#5: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 403 / Source method: isolated from a natural source / Formula: H2O

-
Details

Compound detailsENGINEERED RESIDUE IN CHAIN A, TYR 132 TO PHE ENGINEERED RESIDUE IN CHAIN D, TYR 132 TO PHE
Sequence detailsTRANSPOSASE HAS Y132F MUTATION. DNA DERIVES FROM DEINOCOCCUS RADIODURANS IDRA2 TRANPOSON INTERNAL SEQUENCE

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.68 Å3/Da / Density % sol: 53.9 % / Description: NONE
Crystal growTemperature: 292 K / pH: 4.8
Details: COMPLEX BUFFER: 35MM TRIS-HCL PH 8.0 0.15M NACL, 10MM MGCL2, 0.5 MM TCEP. PRECIPITATING AGENT: 10MM CDCL2, 0.1M NA-ACETATE PH 4.8, 14% PEG4000. PROTEIN AT 9MG/ML IN COMPLEX BUFFER WAS MIXED ...Details: COMPLEX BUFFER: 35MM TRIS-HCL PH 8.0 0.15M NACL, 10MM MGCL2, 0.5 MM TCEP. PRECIPITATING AGENT: 10MM CDCL2, 0.1M NA-ACETATE PH 4.8, 14% PEG4000. PROTEIN AT 9MG/ML IN COMPLEX BUFFER WAS MIXED WITH LE27 AND T5G. PROTEIN AND DNA OLIGONUCLEOTIDES WERE MIXED IN THE RATIO 1:1.1:1.3. EQUAL VOLUMES OF THIS COMPLEX AND PRECIPITATING AGENT WAS MIXED AT 19 C. CRYOPROTECTION IN 20% V/V GLYCEROL.

-
Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: May 2, 2008 / Details: MULTILAYER MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→30 Å / Num. obs: 44818 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 7.44 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 13.4
Reflection shellResolution: 1.9→1.95 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.19 / Mean I/σ(I) obs: 6.91 / % possible all: 99.1

-
Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2XM3

2xm3


Resolution: 1.9→30 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 10000 / Cross valid method: THROUGHOUT / σ(F): 0
Details: AS THE CRYSTALS WERE GROWN IN THE PRESENCE OF BOTH MG2+ AND CD2+, SOME METAL-ION BINDING SITES CONTAINED BOTH AT THE SAME POSITION WITH PARTIAL OCCUPANCIES. THIS WAS OBSERVED IN FO-FC ...Details: AS THE CRYSTALS WERE GROWN IN THE PRESENCE OF BOTH MG2+ AND CD2+, SOME METAL-ION BINDING SITES CONTAINED BOTH AT THE SAME POSITION WITH PARTIAL OCCUPANCIES. THIS WAS OBSERVED IN FO-FC DIFFERENCE MAPS AND ANOMALOUS DIFFERENCE MAPS.
RfactorNum. reflection% reflectionSelection details
Rfree0.2094 904 2 %RANDOM
Rwork0.1805 ---
obs0.1805 44616 98.8 %-
Solvent computationSolvent model: FLAT MODE / Bsol: 42.5371 Å2 / ksol: 0.351729 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-2.976 Å20 Å20 Å2
2---3.003 Å20 Å2
3---0.027 Å2
Refinement stepCycle: LAST / Resolution: 1.9→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2109 1338 21 403 3871
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.018671
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.9573
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2DNA-RNA_REP_NOPUCKERS.PARAMDNA-RNA.TOP
X-RAY DIFFRACTION3CD6_XPLOR_H.PARCD6_XPLOR_H.TOP
X-RAY DIFFRACTION4ACY_XPLOR.PARACY_XPLOR.TOP
X-RAY DIFFRACTION5PARAM19.SOLTOPH19_MOD.SOL

+
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