[English] 日本語
Yorodumi
- PDB-2o5e: Structure of E. coli topoisomerase III in complex with an 8-base ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2o5e
TitleStructure of E. coli topoisomerase III in complex with an 8-base single stranded oligonucleotide. Frozen in glucose pH 7.0
Components
  • 5'-D(*CP*GP*CP*AP*AP*CP*TP*T)-3'
  • DNA topoisomerase 3
KeywordsISOMERASE/DNA / topoisomerase type IA complex with ssDNA / ISOMERASE-DNA COMPLEX
Function / homology
Function and homology information


cytoplasmic replication fork / sequence-specific single stranded DNA binding / chromosome separation / DNA topoisomerase / DNA topoisomerase type I (single strand cut, ATP-independent) activity / DNA topological change / DNA-templated DNA replication / DNA recombination / DNA repair / magnesium ion binding
Similarity search - Function
DNA topoisomerase III / Topoisomerase I, domain 3 / DNA topoisomerase 3-like, TOPRIM domain / Topoisomerase I; domain 2 / Topoisomerase I, domain 2 / Rossmann fold - #140 / Topoisomerase I; domain 4 / Topoisomerase I, domain 4 / Topoisomerase I; domain 3 / DNA topoisomerase, type IA ...DNA topoisomerase III / Topoisomerase I, domain 3 / DNA topoisomerase 3-like, TOPRIM domain / Topoisomerase I; domain 2 / Topoisomerase I, domain 2 / Rossmann fold - #140 / Topoisomerase I; domain 4 / Topoisomerase I, domain 4 / Topoisomerase I; domain 3 / DNA topoisomerase, type IA / DNA topoisomerase, type IA, central region, subdomain 2 / DNA topoisomerase, type IA, active site / Topoisomerase (Topo) IA-type active site signature. / Topoisomerase (Topo) IA-type catalytic domain profile. / DNA topoisomerase, type IA, domain 2 / DNA topoisomerase, type IA, DNA-binding domain / DNA topoisomerase, type IA, central / DNA topoisomerase, type IA, central region, subdomain 1 / DNA topoisomerase, type IA, central region, subdomain 3 / DNA topoisomerase, type IA, core domain / DNA topoisomerase / Bacterial DNA topoisomeraes I ATP-binding domain / Bacterial DNA topoisomerase I DNA-binding domain / TOPRIM / Toprim domain / Toprim domain profile. / TOPRIM domain / Distorted Sandwich / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
THYMINE / DNA / DNA topoisomerase 3
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsChangela, A. / DiGate, R.J. / Mondragon, A.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: Structural Studies of E. coli Topoisomerase III-DNA Complexes Reveal a Novel Type IA Topoisomerase-DNA Conformational Intermediate.
Authors: Changela, A. / Digate, R.J. / Mondragon, A.
History
DepositionDec 5, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 3, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Aug 30, 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 / 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 / _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: 5'-D(*CP*GP*CP*AP*AP*CP*TP*T)-3'
D: 5'-D(*CP*GP*CP*AP*AP*CP*TP*T)-3'
A: DNA topoisomerase 3
B: DNA topoisomerase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)153,2747
Polymers153,0774
Non-polymers1973
Water2,648147
1
C: 5'-D(*CP*GP*CP*AP*AP*CP*TP*T)-3'
A: DNA topoisomerase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,6094
Polymers76,5382
Non-polymers712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: 5'-D(*CP*GP*CP*AP*AP*CP*TP*T)-3'
B: DNA topoisomerase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,6643
Polymers76,5382
Non-polymers1261
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)102.260, 102.260, 445.610
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
DetailsComplex of E. coli topoisomerase III with DNA. Two molecules in the asymmetric unit in the same conformation.

-
Components

#1: DNA chain 5'-D(*CP*GP*CP*AP*AP*CP*TP*T)-3'


Mass: 2386.593 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Protein DNA topoisomerase 3 / DNA topoisomerase III


Mass: 74151.680 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: topB / Plasmid: pET21 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P14294, EC: 5.99.1.2
#3: Chemical ChemComp-TDR / THYMINE


Mass: 126.113 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H6N2O2
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 147 / 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: 3.8 Å3/Da / Density % sol: 67.62 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 1.5 M (NH4)SO4, 0.1M Sodium citrate, 0.5 NaCl, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Components of the solutions
IDNameCrystal-IDSol-ID
1(NH4)SO411
2Sodium citrate11
3NaCl11
4HOH11
5(NH4)SO412
6Sodium citrate12
7NaCl12
8HOH12

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 5ID-B / Wavelength: 0.9479 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jan 15, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9479 Å / Relative weight: 1
ReflectionResolution: 2.5→29.132 Å / Num. obs: 79675 / % possible obs: 96.5 % / Redundancy: 4 % / Rmerge(I) obs: 0.06 / Rsym value: 0.06 / Net I/σ(I): 8.7
Reflection shellResolution: 2.5→2.56 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.328 / Mean I/σ(I) obs: 2.3 / Num. measured all: 14007 / Num. unique all: 5552 / Rsym value: 0.328 / % possible all: 93

-
Processing

Software
NameVersionClassificationNB
SCALAdata scaling
REFMAC5.2.0019refinement
PDB_EXTRACT2data extraction
MAR345345DTBdata collection
XDSdata reduction
CCP4(SCALA)data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1D6M, 1I7D

1d6m

1i7d


Resolution: 2.5→29.132 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.916 / SU B: 16.85 / SU ML: 0.199 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.312 / ESU R Free: 0.25 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26 3992 5 %RANDOM
Rwork0.217 ---
obs0.219 79661 95.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 45.063 Å2
Baniso -1Baniso -2Baniso -3
1-0.55 Å20 Å20 Å2
2--0.55 Å20 Å2
3----1.1 Å2
Refinement stepCycle: LAST / Resolution: 2.5→29.132 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10062 276 11 147 10496
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.02210601
X-RAY DIFFRACTIONr_angle_refined_deg1.2471.99314426
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.63551261
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.84623.353501
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.878151771
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8581598
X-RAY DIFFRACTIONr_chiral_restr0.0840.21593
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.028035
X-RAY DIFFRACTIONr_nbd_refined0.2090.24327
X-RAY DIFFRACTIONr_nbtor_refined0.3040.27137
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1460.2353
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1720.247
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1670.211
X-RAY DIFFRACTIONr_mcbond_it0.5991.56538
X-RAY DIFFRACTIONr_mcangle_it1.019210218
X-RAY DIFFRACTIONr_scbond_it1.35434671
X-RAY DIFFRACTIONr_scangle_it2.224.54208
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.357 283 -
Rwork0.333 5263 -
obs-5546 92.29 %

+
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