[English] 日本語
Yorodumi
- PDB-1bjt: TOPOISOMERASE II RESIDUES 409-1201 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1bjt
TitleTOPOISOMERASE II RESIDUES 409-1201
ComponentsTOPOISOMERASE II
KeywordsTOPOISOMERASE / QUATERNARY CHANGE / DNA-BINDING / DNA TOPOLOGY
Function / homology
Function and homology information


replication fork progression beyond termination site / DNA replication termination region / : / regulation of mitotic recombination / sister chromatid segregation / resolution of meiotic recombination intermediates / synaptonemal complex / SUMOylation of DNA replication proteins / telomere maintenance via recombination / DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) activity ...replication fork progression beyond termination site / DNA replication termination region / : / regulation of mitotic recombination / sister chromatid segregation / resolution of meiotic recombination intermediates / synaptonemal complex / SUMOylation of DNA replication proteins / telomere maintenance via recombination / DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) activity / reciprocal meiotic recombination / DNA topoisomerase (ATP-hydrolysing) / DNA strand elongation involved in DNA replication / DNA topological change / rRNA transcription / chromatin organization / mitochondrion / DNA binding / ATP binding / metal ion binding / identical protein binding / nucleus
Similarity search - Function
Dna Ligase; domain 1 - #30 / Topoisomerase II; domain 5 / Topoisomerase II, domain 5 / Topoisomerase, domain 3 / Topoisomerase; domain 3 / DNA topoisomerase 2, TOPRIM domain / Rossmann fold - #670 / Gyrase A; domain 2 - #40 / C-terminal associated domain of TOPRIM / C-terminal associated domain of TOPRIM ...Dna Ligase; domain 1 - #30 / Topoisomerase II; domain 5 / Topoisomerase II, domain 5 / Topoisomerase, domain 3 / Topoisomerase; domain 3 / DNA topoisomerase 2, TOPRIM domain / Rossmann fold - #670 / Gyrase A; domain 2 - #40 / C-terminal associated domain of TOPRIM / C-terminal associated domain of TOPRIM / DNA topoisomerase II, eukaryotic-type / : / Topoisomerase (Topo) IIA-type catalytic domain profile. / 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, 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 / Toprim domain / DNA topoisomerase, type IIA-like domain superfamily / Toprim domain profile. / TOPRIM domain / Gyrase A; domain 2 / Dna Ligase; domain 1 / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Histidine kinase-like ATPases / Histidine kinase/HSP90-like ATPase superfamily / Ribosomal protein S5 domain 2-type fold, subgroup / Ribosomal protein S5 domain 2-type fold / Alpha-Beta Complex / Rossmann fold / 2-Layer Sandwich / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.5 Å
AuthorsFass, D. / Bogden, C.E. / Berger, J.M.
Citation
Journal: Nat.Struct.Biol. / Year: 1999
Title: Quaternary changes in topoisomerase II may direct orthogonal movement of two DNA strands.
Authors: Fass, D. / Bogden, C.E. / Berger, J.M.
#1: Journal: Nature / Year: 1996
Title: Structure and Mechanism of DNA Topoisomerase II
Authors: Berger, J.M. / Gamblin, S.J. / Harrison, S.C. / Wang, J.C.
#2: Journal: Nature / Year: 1996
Title: Erratum. Structure and Mechanism of DNA Topoisomerase II
Authors: Berger, J.M. / Gamblin, S.J. / Harrison, S.C. / Wang, J.C.
History
DepositionJun 29, 1998Processing site: BNL
Revision 1.0May 4, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: TOPOISOMERASE II


Theoretical massNumber of molelcules
Total (without water)91,8111
Polymers91,8111
Non-polymers00
Water3,909217
1
A: TOPOISOMERASE II

A: TOPOISOMERASE II


Theoretical massNumber of molelcules
Total (without water)183,6212
Polymers183,6212
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area3960 Å2
ΔGint-24 kcal/mol
Surface area67160 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)103.400, 145.700, 161.300
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

-
Components

#1: Protein TOPOISOMERASE II


Mass: 91810.602 Da / Num. of mol.: 1 / Fragment: DNA-BINDING AND CLEAVAGE CORE, RESIDUES 409-1201
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P06786, EC: 5.99.1.3
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 217 / 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: 3.31 Å3/Da / Density % sol: 62.81 %
Crystal growpH: 8 / Details: pH 8.0
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
11-2 %PEG33501drop
220-40 mMTris-Cl1drop
31-2 %PEG33501reservoir
4250-300 mMammonium acetate1reservoir
520-40 mMTris-Cl1reservoir

-
Data collection

DiffractionMean temperature: 118 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 1.1402
DetectorType: FUJI / Detector: IMAGE PLATE / Date: Mar 1, 1997 / Details: MIRRORS
RadiationMonochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1402 Å / Relative weight: 1
ReflectionResolution: 2.5→20 Å / Num. obs: 41611 / % possible obs: 97.6 % / Observed criterion σ(I): -1.5 / Redundancy: 3.5 % / Rmerge(I) obs: 0.06 / Rsym value: 0.06 / Net I/σ(I): 29.8
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.206 / Mean I/σ(I) obs: 4.5 / Rsym value: 0.206 / % possible all: 95

-
Processing

Software
NameVersionClassification
X-PLOR3.851model building
X-PLOR3.851refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.851phasing
RefinementMethod to determine structure: MIR / Resolution: 2.5→14 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Cross valid method: THROUGHOUT / σ(F): 2
Details: THE B FACTORS FOR RESIDUES 653 - 659 ARE VERY HIGH, BUT THE DENSITY FOR THESE RESIDUES WAS SEEN IN SOLVENT-FLATTENED MIR MAPS. THESE RESIDUES HELPED ASSIGN THE CONNECTIVITY BETWEEN DOMAINS IN THE DIMER.
RfactorNum. reflection% reflectionSelection details
Rfree0.269 2905 7.2 %RANDOM
Rwork0.227 ---
obs0.227 40597 95.2 %-
Refinement stepCycle: LAST / Resolution: 2.5→14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5598 0 0 217 5815
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.594
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.164
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 2.5→2.61 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.3731 373 7.6 %
Rwork0.3487 4515 -
obs--97.4 %
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.164

+
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