[English] 日本語
Yorodumi
- PDB-6f86: Crystal Structure of E. coli GyraseB 24kDa in complex with 4-(4-b... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6f86
TitleCrystal Structure of E. coli GyraseB 24kDa in complex with 4-(4-bromo-1H-pyrazol-1-yl)-6-[(ethylcarbamoyl)amino]-N-(pyridin-3-yl)pyridine-3-carboxamide
ComponentsDNA gyrase subunit B
KeywordsISOMERASE / Binding Sites / DNA Gyrase / inhibitors / pyridine-3-carboxamides / topoisomerase IV
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 / ATP-dependent activity, acting on DNA / DNA-templated DNA replication / chromosome / response to xenobiotic stimulus / response to antibiotic ...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 / ATP-dependent activity, acting on DNA / DNA-templated DNA replication / chromosome / response to xenobiotic stimulus / response to antibiotic / DNA-templated transcription / DNA binding / ATP binding / metal ion binding / cytoplasm / cytosol
Similarity search - Function
: / GyrB, hook / DNA gyrase subunit B insert domain / DNA gyrase B subunit insert domain / DNA gyrase subunit B, TOPRIM domain / 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, subunit B, domain 2 ...: / GyrB, hook / DNA gyrase subunit B insert domain / DNA gyrase B subunit insert domain / DNA gyrase subunit B, TOPRIM domain / 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, 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-like ATPase, C-terminal domain / Heat Shock Protein 90 / 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 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-CWW / DNA gyrase subunit B / DNA gyrase subunit B
Similarity search - Component
Biological speciesEscherichia coli O157:H7 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsNarramore, S.K. / Stevenson, C.E.M. / Lawson, D.M. / Maxwell, A. / Fishwick, C.W.G.
CitationJournal: Bioorg.Med.Chem. / Year: 2019
Title: New insights into the binding mode of pyridine-3-carboxamide inhibitors of E. coli DNA gyrase.
Authors: Narramore, S. / Stevenson, C.E.M. / Maxwell, A. / Lawson, D.M. / Fishwick, C.W.G.
History
DepositionDec 12, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 26, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 10, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.2Aug 7, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: DNA gyrase subunit B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,0792
Polymers22,6481
Non-polymers4301
Water1,892105
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area9050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.340, 99.340, 50.210
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

-
Components

#1: Protein DNA gyrase subunit B


Mass: 22648.422 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli O157:H7 (bacteria) / Gene: gyrB, Z5190, ECs4634 / Production host: Escherichia coli (E. coli)
References: UniProt: P0AES7, UniProt: P0AES6*PLUS, EC: 5.99.1.3
#2: Chemical ChemComp-CWW / 4-(4-bromanylpyrazol-1-yl)-6-(ethylcarbamoylamino)-~{N}-pyridin-3-yl-pyridine-3-carboxamide


Mass: 430.259 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H16BrN7O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 105 / 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: 3.16 Å3/Da / Density % sol: 61.05 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 25-30% PEG400 and 100 mM Hepes pH 6.5.

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 1, 2016
RadiationMonochromator: Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.9→49.67 Å / Num. obs: 22689 / % possible obs: 99.7 % / Redundancy: 9.8 % / Biso Wilson estimate: 21.5 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.194 / Rpim(I) all: 0.065 / Rrim(I) all: 0.205 / Net I/σ(I): 8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.9-1.959.61.52716570.5060.5141.61399
8.5-49.6780.0762880.9960.0270.08199.7

-
Processing

Software
NameVersionClassification
Aimless0.5.17data scaling
REFMACrefinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4URO

4uro


Resolution: 1.9→49.67 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.939 / SU B: 7.098 / SU ML: 0.102 / SU R Cruickshank DPI: 0.1287 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.129 / ESU R Free: 0.116
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2187 1210 5.3 %RANDOM
Rwork0.2031 ---
obs0.2041 21468 99.53 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 82.42 Å2 / Biso mean: 33.643 Å2 / Biso min: 19.99 Å2
Baniso -1Baniso -2Baniso -3
1-0.24 Å20.12 Å20 Å2
2--0.24 Å20 Å2
3----0.77 Å2
Refinement stepCycle: final / Resolution: 1.9→49.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1446 0 27 106 1579
Biso mean--32 41.29 -
Num. residues----187
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0191534
X-RAY DIFFRACTIONr_bond_other_d0.0020.021414
X-RAY DIFFRACTIONr_angle_refined_deg1.531.9622082
X-RAY DIFFRACTIONr_angle_other_deg0.9663.0043265
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6875193
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.15523.69973
X-RAY DIFFRACTIONr_dihedral_angle_3_deg1315255
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.2981512
X-RAY DIFFRACTIONr_chiral_restr0.0870.2232
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021736
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02325
LS refinement shellResolution: 1.9→1.949 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.292 72 -
Rwork0.301 1581 -
all-1653 -
obs--98.69 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.7197-2.76120.191910.275-0.00815.2032-0.07810.2292-0.8224-0.01410.19960.5441.1737-0.0816-0.12150.3183-0.1129-0.01140.2882-0.00520.150266.480122.506442.0655
27.0334-2.0412-4.95843.08640.14037.0223-0.05550.1545-0.05560.10680.21010.30150.098-0.6541-0.15460.0621-0.0587-0.03680.19430.03090.111659.550934.072757.3884
31.28041.3246-0.98382.4681-2.23443.3936-0.10670.1231-0.2659-0.24690.09410.05470.4235-0.14230.01260.0647-0.0554-0.00150.1438-0.01840.184167.928527.118860.0004
41.76220.23111.12962.29240.91716.0575-0.07820.0184-0.173-0.01990.0801-0.05880.35560.1654-0.00190.0631-0.03340.02070.074-0.0050.020873.867228.136860.0012
55.79081.8617-1.98081.94312.78339.38210.01550.2421-0.207-0.11430.0809-0.1318-0.2819-0.0762-0.09640.1619-0.0489-0.00660.1756-0.00540.011570.411634.725640.2629
67.8059-0.4587-2.72950.34280.35512.6939-0.16070.179-0.2476-0.13360.12610.11280.185-0.14070.03470.1412-0.0298-0.04070.17540.02540.128556.591341.41148.6088
710.79642.5125-2.7331.9886-0.69113.8680.1876-0.08030.65530.0890.15310.2464-0.4808-0.0738-0.34070.12080.0055-0.00740.11780.03280.092566.158845.231452.7059
88.5043-1.169-3.39952.99670.18143.4532-0.0809-0.2690.2093-0.05410.0260.1414-0.16090.04670.05490.12640.0175-0.0090.13590.01550.131458.36148.746754.7288
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A15 - 38
2X-RAY DIFFRACTION2A39 - 58
3X-RAY DIFFRACTION3A59 - 120
4X-RAY DIFFRACTION4A121 - 173
5X-RAY DIFFRACTION5A174 - 186
6X-RAY DIFFRACTION6A187 - 197
7X-RAY DIFFRACTION7A198 - 212
8X-RAY DIFFRACTION8A213 - 219

+
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