[English] 日本語
Yorodumi
- PDB-5btd: Crystal structure of a topoisomerase II complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5btd
TitleCrystal structure of a topoisomerase II complex
Components
  • (DNA gyrase subunit ...) x 2
  • (DNA substrate 24-mer ...) x 2
KeywordsIsomerase/DNA / protein-DNA complex / topoisomerase II / Isomerase-DNA complex
Function / homology
Function and homology information


DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) complex / DNA negative supercoiling activity / DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) activity / DNA topoisomerase (ATP-hydrolysing) / DNA topological change / peptidoglycan-based cell wall / DNA-templated DNA replication / chromosome / response to antibiotic / magnesium ion binding ...DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) complex / DNA negative supercoiling activity / DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) activity / DNA topoisomerase (ATP-hydrolysing) / DNA topological change / peptidoglycan-based cell wall / DNA-templated DNA replication / chromosome / response to antibiotic / magnesium ion binding / ATP hydrolysis activity / DNA binding / ATP binding / plasma membrane / cytoplasm
Similarity search - Function
Rossmann fold - #670 / DNA gyrase, subunit A / : / DNA gyrase/topoisomerase IV, subunit A, C-terminal repeat / DNA gyrase/topoisomerase IV, subunit A, C-terminal / DNA gyrase C-terminal domain, beta-propeller / DNA gyrase subunit B, TOPRIM domain / Topoisomerase (Topo) IIA-type catalytic domain profile. / DNA gyrase, subunit B / DNA topoisomerase, type IIA, subunit B ...Rossmann fold - #670 / DNA gyrase, subunit A / : / DNA gyrase/topoisomerase IV, subunit A, C-terminal repeat / DNA gyrase/topoisomerase IV, subunit A, C-terminal / DNA gyrase C-terminal domain, beta-propeller / DNA gyrase subunit B, TOPRIM domain / Topoisomerase (Topo) IIA-type catalytic domain profile. / DNA gyrase, subunit B / DNA topoisomerase, type IIA, subunit B / DNA gyrase B subunit, C-terminal / DNA gyrase B subunit, carboxyl terminus / 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 / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Histidine kinase-like ATPases / Histidine kinase/HSP90-like ATPase / Histidine kinase/HSP90-like ATPase superfamily / EF-hand calcium-binding domain. / Ribosomal protein S5 domain 2-type fold, subgroup / Ribosomal protein S5 domain 2-type fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-GFN / DNA / DNA (> 10) / DNA gyrase subunit B / DNA gyrase subunit A
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.497 Å
AuthorsBlower, T.R. / Williamson, B.H. / Kerns, R.J. / Berger, J.M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)R01-CA077373 United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2016
Title: Crystal structure and stability of gyrase-fluoroquinolone cleaved complexes from Mycobacterium tuberculosis.
Authors: Blower, T.R. / Williamson, B.H. / Kerns, R.J. / Berger, J.M.
History
DepositionJun 3, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 2, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Sep 27, 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 / diffrn_radiation_wavelength / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_alt_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_alt_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.4Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.5Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: DNA gyrase subunit A
B: DNA gyrase subunit B
C: DNA gyrase subunit A
D: DNA gyrase subunit B
E: DNA substrate 24-mer GGTCATGAATGACTATGCACGTAA
F: DNA substrate 24-mer TTACGTGCATAGTCATTCATGACC
G: DNA substrate 24-mer TTACGTGCATAGTCATTCATGACC
H: DNA substrate 24-mer GGTCATGAATGACTATGCACGTAA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)199,28714
Polymers198,4398
Non-polymers8486
Water3,801211
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)107.907, 83.158, 129.203
Angle α, β, γ (deg.)90.000, 108.650, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain C
12chain B
22chain D
13chain E
23chain H
14chain F
24chain G

NCS domain segments:

Component-ID: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-IDBeg label alt-IDEnd label alt-ID
11ILEILEILEILEchain AAA15 - 50114 - 500
21ILEILEILEILEchain CCC15 - 50114 - 500
12ALAALAVALVALchain BBB425 - 6753 - 253
22ASNASNVALVALchain DDD424 - 6752 - 253
13DTDTDADAchain EEE3 - 233 - 23AA
23DTDTDADAchain HHH3 - 233 - 23BB
14DADADCDCchain FFF3 - 233 - 23AA
24DADADCDCchain GGG3 - 233 - 23BB

NCS ensembles :
ID
1
2
3
4
DetailsThe double-stranded DNAs are superposed copies of each other, overlaid in opposite orientations (because directionality could not be resolved). Therefore in reality, rather than in the model, the biological assembly would in fact be hexameric - four proteins and one double-stranded DNA.

-
Components

-
DNA gyrase subunit ... , 2 types, 4 molecules ACBD

#1: Protein DNA gyrase subunit A


Mass: 56209.422 Da / Num. of mol.: 2 / Fragment: GyrA 2-500 with IGSG C-terminal tag
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Strain: ATCC 25618 / H37Rv / Gene: gyrA, Rv0006, MTCY10H4.04 / Plasmid: pET-28b / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2 pLysS / References: UniProt: P9WG47, EC: 5.99.1.3
#2: Protein DNA gyrase subunit B


Mass: 28272.412 Da / Num. of mol.: 2 / Fragment: GyrB 426-675 with N-terminal SNA tag
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Strain: ATCC 25618 / H37Rv / Gene: gyrB, Rv0005, MTCY10H4.03 / Plasmid: pET-28b / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2 pLysS / References: UniProt: P9WG45, EC: 5.99.1.3

-
DNA substrate 24-mer ... , 2 types, 4 molecules EHFG

#3: DNA chain DNA substrate 24-mer GGTCATGAATGACTATGCACGTAA


Mass: 7417.816 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: synthetic construct (others)
#4: DNA chain DNA substrate 24-mer TTACGTGCATAGTCATTCATGACC


Mass: 7319.739 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: synthetic construct (others)

-
Non-polymers , 3 types, 217 molecules

#5: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-GFN / 1-cyclopropyl-6-fluoro-8-methoxy-7-[(3S)-3-methylpiperazin-1-yl]-4-oxo-1,4-dihydroquinoline-3-carboxylic acid / Gatifloxacin


Mass: 375.394 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H22FN3O4 / Comment: antibiotic*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 211 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.77 Å3/Da / Density % sol: 55.56 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop
Details: 100 mM Tris-HCl, 13-15% PEG 4000, 200 mM MgCl2, 6.25% PEG 400
PH range: 7.0 to 8.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.033 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 7, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 2.497→47.394 Å / Num. all: 285133 / Num. obs: 285133 / % possible obs: 99.66 % / Redundancy: 3.8 % / Biso Wilson estimate: 45.58 Å2 / Rmerge F obs: 0.989 / Rmerge(I) obs: 0.1365 / Rrim(I) all: 0.158 / Χ2: 1.015 / Net I/σ(I): 10.36 / Num. measured all: 285078
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Highest resolution (Å)Rmerge F obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible allRmerge(I) obs
2.497-2.5860.2321.12008210929102991.72797.56
2.56-2.630.3170.952069610743105021.42297.81.032
2.63-2.710.4171.21986210274100841.10398.20.802
2.71-2.790.5051.42196231016199690.9398.10.676
2.79-2.880.6231.8618794970995550.71198.40.517
2.88-2.980.7052.2618274944292910.59498.40.432
2.98-3.10.8272.9617771915790260.43698.60.317
3.1-3.220.8813.8416865869385770.34498.70.249
3.22-3.370.9375.2116267840682650.24498.30.177
3.37-3.530.9586.8515599802379220.18398.70.133
3.53-3.720.9798.9614777764375040.13398.20.097
3.72-3.950.98611.314111726671640.10198.60.074
3.95-4.220.99213.7913146677766630.0898.30.058
4.22-4.560.99516.5412284633162240.06298.30.045
4.56-4.990.99518.0511310584057280.05698.10.04
4.99-5.580.99416.8410193524451490.06298.20.045
5.58-6.450.99416.359001464645490.06297.90.045
6.45-7.90.99620.977550387938120.04698.30.033
7.9-11.170.99829.365799303329380.03196.90.022
11.170.99832.283074167815670.02793.40.019

-
Processing

Software
NameVersionClassification
PHENIXrefinement
XSCALEdata scaling
PDB_EXTRACT3.15data extraction
Cootmodel building
PHASERphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5BS8

5bs8


Resolution: 2.497→47.394 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 0.85 / Phase error: 27.72 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2464 7285 5.03 %Random selection
Rwork0.2146 137487 --
obs0.2162 144772 97.94 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 241.92 Å2 / Biso mean: 69.0218 Å2 / Biso min: 19.5 Å2
Refinement stepCycle: final / Resolution: 2.497→47.394 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11538 1640 100 211 13489
Biso mean--48.61 47.15 -
Num. residues----1550
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00413646
X-RAY DIFFRACTIONf_angle_d0.74118759
X-RAY DIFFRACTIONf_chiral_restr0.0312116
X-RAY DIFFRACTIONf_plane_restr0.0032179
X-RAY DIFFRACTIONf_dihedral_angle_d15.4835305
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A5804X-RAY DIFFRACTION5.925TORSIONAL
12C5804X-RAY DIFFRACTION5.925TORSIONAL
21B2968X-RAY DIFFRACTION5.925TORSIONAL
22D2968X-RAY DIFFRACTION5.925TORSIONAL
31E404X-RAY DIFFRACTION5.925TORSIONAL
32H404X-RAY DIFFRACTION5.925TORSIONAL
41F404X-RAY DIFFRACTION5.925TORSIONAL
42G404X-RAY DIFFRACTION5.925TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4968-2.52520.40591880.37184215440388
2.5252-2.55490.36872150.35934502471798
2.5549-2.58610.3752500.35774638488898
2.5861-2.61880.38632930.34414551484498
2.6188-2.65320.38032430.33264611485498
2.6532-2.68960.31522090.32394619482898
2.6896-2.7280.34652290.31654559478898
2.728-2.76870.33822180.32294679489798
2.7687-2.8120.34382300.30944516474698
2.812-2.85810.33052550.29044628488399
2.8581-2.90740.32222680.30354584485298
2.9074-2.96020.31612860.28814666495298
2.9602-3.01710.29822220.27444557477999
3.0171-3.07870.31532510.2684635488699
3.0787-3.14570.31642740.26644569484399
3.1457-3.21880.23282620.25744584484698
3.2188-3.29930.28972160.23494633484998
3.2993-3.38850.29352550.22964618487399
3.3885-3.48810.24932380.22014667490599
3.4881-3.60070.25332580.20824591484998
3.6007-3.72930.23492140.19214552476698
3.7293-3.87860.19992500.18144671492199
3.8786-4.0550.22852590.1744599485898
4.055-4.26870.16792550.16054566482199
4.2687-4.53590.19752910.15164580487198
4.5359-4.88580.17082410.15224566480798
4.8858-5.37690.19562140.1574642485698
5.3769-6.15350.21572240.18124587481198
6.1535-7.74730.21812350.17814622485798
7.7473-47.40280.18972420.16294480472296

+
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