[English] 日本語
Yorodumi
- PDB-8wwo: Crystal structure of the AFSV topoisomerase ATPase domain in comp... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8wwo
TitleCrystal structure of the AFSV topoisomerase ATPase domain in complex with AMPPNP
ComponentsDNA topoisomerase 2Topoisomerase
KeywordsVIRAL PROTEIN / topoisomerase
Function / homology
Function and homology information


DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) activity / DNA topoisomerase (ATP-hydrolysing) / DNA topological change / host cell cytoplasm / DNA binding / ATP binding / metal ion binding / cytoplasm
Similarity search - Function
DNA topoisomerase II, eukaryotic-type / C-terminal associated domain of TOPRIM / C-terminal associated domain of TOPRIM / DNA topoisomerase, type IIA, alpha-helical domain superfamily / DNA topoisomerase, type IIA, domain A / DNA topoisomerase, type IIA, domain A, alpha-beta / DNA gyrase/topoisomerase IV, subunit A / DNA Topoisomerase IV / DNA topoisomerase, type IIA / DNA topoisomerase, type IIA, conserved site ...DNA topoisomerase II, eukaryotic-type / C-terminal associated domain of TOPRIM / C-terminal associated domain of TOPRIM / DNA topoisomerase, type IIA, alpha-helical domain superfamily / DNA topoisomerase, type IIA, domain A / DNA topoisomerase, type IIA, domain A, alpha-beta / DNA gyrase/topoisomerase IV, subunit A / DNA Topoisomerase IV / DNA topoisomerase, type IIA / DNA topoisomerase, type IIA, conserved site / DNA topoisomerase II signature. / TopoisomeraseII / DNA topoisomerase, type IIA, subunit B, C-terminal / DNA topoisomerase, type IIA-like domain superfamily / Histidine kinase/HSP90-like ATPase superfamily / Ribosomal protein S5 domain 2-type fold, subgroup / Ribosomal protein S5 domain 2-type fold
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / DNA topoisomerase 2
Similarity search - Component
Biological speciesAfrican swine fever virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsKuang, W. / Deng, Z.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Crystal of the AFSV topoisomerase ATPase domain in complex with AMPPNP
Authors: Deng, Z.
History
DepositionOct 26, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 21, 2024Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: DNA topoisomerase 2
B: DNA topoisomerase 2
C: DNA topoisomerase 2
D: DNA topoisomerase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)186,81512
Polymers184,6934
Non-polymers2,1228
Water19,3301073
1
A: DNA topoisomerase 2
hetero molecules

D: DNA topoisomerase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,4086
Polymers92,3472
Non-polymers1,0614
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_655x+1,y,z1
Buried area7160 Å2
ΔGint-45 kcal/mol
Surface area32360 Å2
MethodPISA
2
B: DNA topoisomerase 2
C: DNA topoisomerase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,4086
Polymers92,3472
Non-polymers1,0614
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7340 Å2
ΔGint-45 kcal/mol
Surface area31950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.658, 85.658, 212.071
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number144
Space group name H-MP31
Space group name HallP31
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 1 through 76 or (resid 77...
d_2ens_1(chain "B" and (resid 1 through 76 or (resid 77...
d_3ens_1(chain "C" and (resid 1 through 36 or (resid 37...
d_4ens_1(chain "D" and (resid 1 through 76 or (resid 77...

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11METMETSERSERAA1 - 4031 - 403
d_12ANPANPANPANPAE501
d_21METMETSERSERBB1 - 4031 - 403
d_22ANPANPANPANPBG501
d_31METMETSERSERCC1 - 4031 - 403
d_32ANPANPANPANPCI501
d_41METMETSERSERDD1 - 4031 - 403
d_42ANPANPANPANPDK501

-
Components

#1: Protein
DNA topoisomerase 2 / Topoisomerase


Mass: 46173.301 Da / Num. of mol.: 4 / Fragment: ATPase domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) African swine fever virus / Gene: P1192R CDS / Production host: Komagataella pastoris (fungus) / References: UniProt: A0A2X0THW2
#2: Chemical
ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1073 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.54 Å3/Da / Density % sol: 51.55 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, hanging drop
Details: 0.2M Ammonium sulfate, 0.1M HEPES pH 7.5, 22.5% PEG 3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 20, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 87831 / % possible obs: 96.5 % / Redundancy: 3 % / Biso Wilson estimate: 25.42 Å2 / CC1/2: 0.994 / Net I/σ(I): 11.1
Reflection shellResolution: 2.2→2.28 Å / Num. unique obs: 8623 / CC1/2: 0.731

-
Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→24.96 Å / SU ML: 0.2204 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 22.3169
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2209 4218 4.98 %
Rwork0.1757 80481 -
obs0.1779 84699 96.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 29.65 Å2
Refinement stepCycle: LAST / Resolution: 2.2→24.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12261 0 128 1073 13462
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.009612649
X-RAY DIFFRACTIONf_angle_d1.216917172
X-RAY DIFFRACTIONf_chiral_restr0.06632012
X-RAY DIFFRACTIONf_plane_restr0.01342127
X-RAY DIFFRACTIONf_dihedral_angle_d11.20411709
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AAX-RAY DIFFRACTIONTorsion NCS0.378034327377
ens_1d_3AAX-RAY DIFFRACTIONTorsion NCS0.377862596766
ens_1d_4AAX-RAY DIFFRACTIONTorsion NCS0.342406219808
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.230.27941250.22712696X-RAY DIFFRACTION97.31
2.23-2.260.27151170.2252799X-RAY DIFFRACTION98.12
2.26-2.280.23471240.22892730X-RAY DIFFRACTION98.24
2.28-2.310.30411300.21952792X-RAY DIFFRACTION97.86
2.31-2.340.22911380.21342616X-RAY DIFFRACTION97.76
2.34-2.370.27761610.21042750X-RAY DIFFRACTION97.65
2.38-2.410.25241560.20082679X-RAY DIFFRACTION97.49
2.41-2.440.27641600.20062705X-RAY DIFFRACTION97.48
2.44-2.480.27151460.20872677X-RAY DIFFRACTION97.11
2.48-2.520.27341830.1962701X-RAY DIFFRACTION97.2
2.52-2.570.19771610.20292615X-RAY DIFFRACTION96.79
2.57-2.610.21811580.1972676X-RAY DIFFRACTION96.99
2.61-2.660.21261670.19212683X-RAY DIFFRACTION96.87
2.66-2.720.22071060.18452720X-RAY DIFFRACTION96.81
2.72-2.780.24771590.17922694X-RAY DIFFRACTION97.17
2.78-2.840.2411320.17612712X-RAY DIFFRACTION97.1
2.84-2.910.21971060.18332715X-RAY DIFFRACTION97.14
2.91-2.990.22931290.18952626X-RAY DIFFRACTION95.73
2.99-3.080.23631240.17812742X-RAY DIFFRACTION96.5
3.08-3.180.3251410.18952696X-RAY DIFFRACTION96.4
3.18-3.290.21071530.16742675X-RAY DIFFRACTION96.58
3.29-3.420.23741910.16652598X-RAY DIFFRACTION96.21
3.42-3.580.25891310.16092703X-RAY DIFFRACTION96.1
3.58-3.770.22371530.15372627X-RAY DIFFRACTION96.13
3.77-40.15081220.15022665X-RAY DIFFRACTION95.48
4-4.310.18191400.14062671X-RAY DIFFRACTION95.13
4.31-4.740.17561320.13792633X-RAY DIFFRACTION94.69
4.74-5.420.16431350.15292631X-RAY DIFFRACTION95.15
5.42-6.810.18311230.19262665X-RAY DIFFRACTION95.19
6.81-24.960.18081150.17142589X-RAY DIFFRACTION92.26

+
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