[English] 日本語
Yorodumi
- PDB-9imj: Bacteriophage T6 topoisomerase II ATPase domain crystal strcuture -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9imj
TitleBacteriophage T6 topoisomerase II ATPase domain crystal strcuture
ComponentsDNA topoisomerase (ATP-hydrolyzing)
KeywordsISOMERASE / topoisomerase II ATPase domain
Function / homology
Function and homology information


sister chromatid segregation / DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) activity / DNA topoisomerase (ATP-hydrolysing) / DNA topological change / DNA binding / ATP binding
Similarity search - Function
: / DNA topoisomerase, type IIA, subunit B, domain 2 / DNA gyrase B / 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-, DNA gyrase B-, and HSP90-like ATPase ...: / DNA topoisomerase, type IIA, subunit B, domain 2 / DNA gyrase B / 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-, DNA gyrase B-, and HSP90-like ATPase / Histidine kinase-like ATPases / Histidine kinase/HSP90-like ATPase / 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 (ATP-hydrolyzing)
Similarity search - Component
Biological speciesEnterobacteria phage T6 (virus)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsXin, Y.H. / Chen, Y.T.
Funding support China, 1items
OrganizationGrant numberCountry
Chinese Academy of Sciences China
CitationJournal: To be published
Title: Bacteriophage T6 topoisomerase II ATPase domain crystal strcuture
Authors: Xin, Y.H. / Chen, Y.T.
History
DepositionJul 3, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Sep 25, 2024Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: DNA topoisomerase (ATP-hydrolyzing)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,2153
Polymers43,6851
Non-polymers5312
Water32418
1
A: DNA topoisomerase (ATP-hydrolyzing)
hetero molecules

A: DNA topoisomerase (ATP-hydrolyzing)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,4316
Polymers87,3702
Non-polymers1,0614
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z+1/31
Buried area7870 Å2
ΔGint-37 kcal/mol
Surface area29720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.989, 90.989, 102.900
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

-
Components

#1: Protein DNA topoisomerase (ATP-hydrolyzing)


Mass: 43684.969 Da / Num. of mol.: 1 / Fragment: ATPase domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage T6 (virus) / Gene: EcT6_00003 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A346FJ89, DNA topoisomerase (ATP-hydrolysing)
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C10H17N6O12P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 18 / 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: 2.81 Å3/Da / Density % sol: 56.3 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: PEG3350, succinic acid

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-X / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Jun 27, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 13967 / % possible obs: 100 % / Redundancy: 16.1 % / CC1/2: 0.998 / CC star: 0.999 / Rmerge(I) obs: 0.101 / Rpim(I) all: 0.026 / Rrim(I) all: 0.104 / Χ2: 2.127 / Net I/σ(I): 12.1 / Num. measured all: 225456
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
2.7-2.7515.80.7366850.9720.9930.1890.761.053100
2.75-2.8160.6936690.9840.9960.1780.7161.046100
2.8-2.8516.10.637130.9830.9960.1610.651.064100
2.85-2.9116.30.5116740.9860.9970.130.5281.064100
2.91-2.9716.40.4916700.9860.9960.1240.5061.17100
2.97-3.0416.40.3567210.9930.9980.0910.3671.304100
3.04-3.1216.80.2926680.9950.9990.0730.3011.477100
3.12-3.216.60.2586970.9950.9990.0650.2661.525100
3.2-3.316.50.26680.9960.9990.0510.2061.688100
3.3-3.416.70.1696960.9970.9990.0430.1741.975100
3.4-3.5216.60.1457020.99910.0370.152.271100
3.52-3.6616.50.1246910.99810.0310.1282.514100
3.66-3.8316.30.1116950.9980.9990.0280.1152.914100
3.83-4.0316.20.0946970.99810.0240.0973.006100
4.03-4.2916.10.0867070.99810.0220.0893.171100
4.29-4.6215.80.0756990.99910.0190.0773.51100
4.62-5.0816.20.0727070.99910.0180.0743.095100
5.08-5.81160.0657060.99910.0170.0672.905100
5.81-7.3215.90.0597290.99910.0150.0612.719100
7.32-50140.0477730.9980.9990.0130.0493.00599.2

-
Processing

Software
NameVersionClassification
PHENIXv1.20refinement
HKL-2000data scaling
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→36.79 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 31.8 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2895 594 5.05 %
Rwork0.2333 --
obs0.236 11766 93.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.8→36.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2970 0 32 18 3020
Refine LS restraintsType: f_plane_restr / Dev ideal: 0.01 / Number: 530
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-3.080.48971450.36312714X-RAY DIFFRACTION93
3.08-3.530.33231660.27052670X-RAY DIFFRACTION91
3.53-4.440.28481330.22082796X-RAY DIFFRACTION94
4.44-36.790.21971500.19792992X-RAY DIFFRACTION97

+
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