[English] 日本語
Yorodumi
- PDB-8df9: Structure of M. kandleri topoisomerase V in complex with DNA. 38 ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8df9
TitleStructure of M. kandleri topoisomerase V in complex with DNA. 38 base pair asymmetric DNA complex
Components
  • (DNA (33-MER)) x 2
  • DNA (5'-D(P*GP*CP*CP*TP*GP*CP*AP*CP*GP*AP*AP*GP*TP*AP*AP*GP*C)-3')
  • DNA (5'-D(P*GP*CP*CP*TP*GP*CP*AP*CP*GP*AP*AP*GP*TP*AP*AP*GP*CP*A)-3')
  • DNA (5'-D(P*TP*GP*CP*TP*TP*AP*CP*TP*TP*CP*GP*TP*GP*CP*AP*GP*GP*CP*CP*A)-3')
  • Topoisomerase V
KeywordsDNA BINDING PROTEIN/DNA / Topoisomerase V Type IC / Abasic DNA / DNA BINDING PROTEIN / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


isomerase activity / DNA repair / DNA binding / metal ion binding
Similarity search - Function
: / Topoisomerase V, second (HhH)2 tandem domain / DNA topoisomerase V, catalytic domain superfamily / Winged helix-turn-helix DNA-binding / RuvA domain 2-like / Helix-hairpin-helix domain / Helix-hairpin-helix DNA-binding motif, class 1 / Helix-hairpin-helix DNA-binding motif class 1 / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
: / DNA / DNA (> 10) / Topoisomerase V
Similarity search - Component
Biological speciesMethanopyrus kandleri (archaea)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 3.24 Å
AuthorsOsterman, A. / Mondragon, A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM118108 United States
CitationJournal: Elife / Year: 2022
Title: Structures of topoisomerase V in complex with DNA reveal unusual DNA binding mode and novel relaxation mechanism.
Authors: Osterman, A. / Mondragon, A.
History
DepositionJun 21, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 31, 2022Provider: repository / Type: Initial release
Revision 1.1Feb 14, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Topoisomerase V
B: Topoisomerase V
S: DNA (33-MER)
T: DNA (33-MER)
U: DNA (5'-D(P*GP*CP*CP*TP*GP*CP*AP*CP*GP*AP*AP*GP*TP*AP*AP*GP*C)-3')
V: DNA (5'-D(P*TP*GP*CP*TP*TP*AP*CP*TP*TP*CP*GP*TP*GP*CP*AP*GP*GP*CP*CP*A)-3')
W: DNA (5'-D(P*GP*CP*CP*TP*GP*CP*AP*CP*GP*AP*AP*GP*TP*AP*AP*GP*CP*A)-3')
X: DNA (5'-D(P*TP*GP*CP*TP*TP*AP*CP*TP*TP*CP*GP*TP*GP*CP*AP*GP*GP*CP*CP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)237,87922
Polymers237,5098
Non-polymers37014
Water54030
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)193.751, 193.751, 245.979
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 2 through 828 or resid 835 through 852))
d_2ens_1(chain "B" and (resid 2 through 617 or resid 690 through 852))
d_1ens_2chain "U"
d_2ens_2(chain "W" and resid 2 through 18)
d_1ens_3(chain "V" and (resid 20 through 38 or (resid 39...
d_2ens_3chain "X"

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1ALAALAA1 - 755
d_12ens_1ALAGLYA762 - 779
d_21ens_1ALALYSB1 - 616
d_22ens_1GLUGLYB689 - 845
d_11ens_2DGDCQ
d_21ens_2DGDCS
d_11ens_3DTDTR
d_21ens_3DTDTT

NCS ensembles :
ID
ens_1
ens_2
ens_3

NCS oper:
IDCodeMatrixVector
1given(-0.990067428864, 0.0517304157731, -0.13073044935), (-0.0948326369972, 0.440749583972, 0.892606618387), (0.103794302655, 0.896138252901, -0.431466075635)14.9656118676, -5.17135139595, 1.98877755996
2given(0.011385798483, 0.910446436547, -0.413470252585), (0.825018809348, 0.225083690038, 0.518344766252), (0.564990555509, -0.347022504542, -0.748572677518)59.3577305808, -14.8968441407, -83.3371892737
3given(0.0530424250418, 0.88040200818, -0.471252379451), (0.850202655929, 0.207712052243, 0.483746986766), (0.52377661746, -0.426319137907, -0.737502574678)53.2811716879, -17.5963537474, -87.7734176536

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein Topoisomerase V / Winged helix-turn-helix transcriptional regulator


Mass: 97110.445 Da / Num. of mol.: 2 / Mutation: K809A, K820A, K831A, K835A, K846A, K851A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanopyrus kandleri (archaea) / Gene: top5, HA336_03250 / Production host: Escherichia coli (E. coli) / References: UniProt: Q977W1

-
DNA chain , 5 types, 6 molecules STUVXW

#2: DNA chain DNA (33-MER)


Mass: 10203.584 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (33-MER)


Mass: 10096.495 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: DNA chain DNA (5'-D(P*GP*CP*CP*TP*GP*CP*AP*CP*GP*AP*AP*GP*TP*AP*AP*GP*C)-3')


Mass: 5221.400 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#5: DNA chain DNA (5'-D(P*TP*GP*CP*TP*TP*AP*CP*TP*TP*CP*GP*TP*GP*CP*AP*GP*GP*CP*CP*A)-3')


Mass: 6115.951 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#6: DNA chain DNA (5'-D(P*GP*CP*CP*TP*GP*CP*AP*CP*GP*AP*AP*GP*TP*AP*AP*GP*CP*A)-3')


Mass: 5534.607 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

-
Non-polymers , 3 types, 44 molecules

#7: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Mg
#8: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 30 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 4.87 Å3/Da / Density % sol: 74.76 %
Crystal growTemperature: 303 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: Protein was mixed with the annealed oligonucleotide using a stoichiometric ratio of 1.25:1 DNA to protein in 1X DNA binding buffer. Reactions were incubated for thirty minutes at 65 C. ...Details: Protein was mixed with the annealed oligonucleotide using a stoichiometric ratio of 1.25:1 DNA to protein in 1X DNA binding buffer. Reactions were incubated for thirty minutes at 65 C. Crystals started to appear within minutes of setting up the trays in 1:1 or 2:1 well to complex ratio. Well solution: 10% PEG 600, 50 mM sodium succinate pH 5.5, 200 mM potassium chloride, 10 mM magnesium chloride, 1 mM spermine

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97856 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Mar 14, 2018 / Details: monochromator
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 3.24→39.3 Å / Num. obs: 52587 / % possible obs: 70.4 % / Redundancy: 8.2 % / Biso Wilson estimate: 121.81 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.093 / Rrim(I) all: 0.1 / Net I/σ(I): 13.5
Reflection shellResolution: 3.24→3.601 Å / Redundancy: 9.4 % / Rmerge(I) obs: 1.48 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 2629 / CC1/2: 0.58 / Rrim(I) all: 1.567 / % possible all: 13.2

-
Processing

Software
NameVersionClassification
BUSTERrefinement
PHENIX1.19.1_4122refinement
XDSdata reduction
STARANISOdata scaling
SHARPphasing
RefinementMethod to determine structure: SIRAS / Resolution: 3.24→39.28 Å / SU ML: 0.3447 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.8056
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2656 2599 4.95 %
Rwork0.2346 49867 -
obs0.2362 52466 70.33 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 141.21 Å2
Refinement stepCycle: LAST / Resolution: 3.24→39.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13014 2871 44 0 15929
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003916442
X-RAY DIFFRACTIONf_angle_d0.561722799
X-RAY DIFFRACTIONf_chiral_restr0.0372523
X-RAY DIFFRACTIONf_plane_restr0.00412483
X-RAY DIFFRACTIONf_dihedral_angle_d20.86756559
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONTorsion NCS1.83125288934
ens_2d_2UX-RAY DIFFRACTIONTorsion NCS1.27918545827
ens_3d_2VX-RAY DIFFRACTIONTorsion NCS2.12223141682
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.24-3.30.288130.471295X-RAY DIFFRACTION2.56
3.3-3.360.3256110.5044216X-RAY DIFFRACTION5.93
3.36-3.430.398220.434350X-RAY DIFFRACTION9.62
3.43-3.510.3665320.3623702X-RAY DIFFRACTION19.03
3.51-3.590.389600.3661952X-RAY DIFFRACTION26.16
3.59-3.680.3246720.31431398X-RAY DIFFRACTION38.05
3.68-3.780.34041170.29951913X-RAY DIFFRACTION52.31
3.78-3.890.32231490.29322890X-RAY DIFFRACTION78.16
3.89-4.010.3011910.28793660X-RAY DIFFRACTION98.62
4.01-4.160.28041810.27023699X-RAY DIFFRACTION100
4.16-4.320.25442110.24613701X-RAY DIFFRACTION100
4.32-4.520.25111790.23933722X-RAY DIFFRACTION99.97
4.52-4.760.27331990.22713720X-RAY DIFFRACTION100
4.76-5.060.28951630.22783765X-RAY DIFFRACTION100
5.06-5.450.25212000.23883726X-RAY DIFFRACTION100
5.45-5.990.28411800.26373789X-RAY DIFFRACTION100
5.99-6.860.27252290.25863773X-RAY DIFFRACTION100
6.86-8.620.24021840.21543844X-RAY DIFFRACTION100
8.62-39.280.24252160.18773952X-RAY DIFFRACTION98.53

+
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