[English] 日本語
Yorodumi
- PDB-4p8o: S. aureus gyrase bound to an aminobenzimidazole urea inhibitor -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4p8o
TitleS. aureus gyrase bound to an aminobenzimidazole urea inhibitor
ComponentsDNA gyrase subunit B
KeywordsISOMERASE / antibacterial / gram-positive / gyrase / topoisomerase / Staphylococcus aureus
Function / homology
Function and homology information


DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) activity / DNA topoisomerase (ATP-hydrolysing) / DNA topological change / DNA-templated DNA replication / chromosome / DNA binding / ATP binding / metal ion binding / cytoplasm
Similarity search - Function
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. ...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 / 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-883 / DNA gyrase subunit B
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.4 Å
AuthorsJacobs, M.D.
CitationJournal: J.Med.Chem. / Year: 2014
Title: Second-generation antibacterial benzimidazole ureas: discovery of a preclinical candidate with reduced metabolic liability.
Authors: Grillot, A.L. / Tiran, A.L. / Shannon, D. / Krueger, E. / Liao, Y. / O'Dowd, H. / Tang, Q. / Ronkin, S. / Wang, T. / Waal, N. / Li, P. / Lauffer, D. / Sizensky, E. / Tanoury, J. / Perola, E. ...Authors: Grillot, A.L. / Tiran, A.L. / Shannon, D. / Krueger, E. / Liao, Y. / O'Dowd, H. / Tang, Q. / Ronkin, S. / Wang, T. / Waal, N. / Li, P. / Lauffer, D. / Sizensky, E. / Tanoury, J. / Perola, E. / Grossman, T.H. / Doyle, T. / Hanzelka, B. / Jones, S. / Dixit, V. / Ewing, N. / Liao, S. / Boucher, B. / Jacobs, M. / Bennani, Y. / Charifson, P.S.
History
DepositionMar 31, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 29, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 26, 2014Group: Database references
Revision 1.2Sep 30, 2015Group: Data collection
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: DNA gyrase subunit B
B: DNA gyrase subunit B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,6454
Polymers42,8902
Non-polymers7552
Water2,936163
1
A: DNA gyrase subunit B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,8222
Polymers21,4451
Non-polymers3771
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: DNA gyrase subunit B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,8222
Polymers21,4451
Non-polymers3771
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)143.460, 55.730, 50.800
Angle α, β, γ (deg.)90.000, 100.420, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-432-

HOH

-
Components

#1: Protein DNA gyrase subunit B


Mass: 21444.949 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: ATPase domain with loop deletion / Source: (gene. exp.) Staphylococcus aureus (bacteria) / Strain: 04-02981 / Gene: gyrB, SAR0005 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q6GKU0, EC: 5.99.1.3
#2: Chemical ChemComp-883 / 1-ethyl-3-[5-(5-fluoropyridin-3-yl)-7-(pyrimidin-2-yl)-1H-benzimidazol-2-yl]urea


Mass: 377.375 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H16FN7O
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 163 / 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: 2.36 Å3/Da / Density % sol: 47.95 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 2M Ammonium sulfate, 100 mM Tris pH 8.0, 5-10% MPD

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 21, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→30 Å / Num. obs: 15076 / % possible obs: 96.9 % / Redundancy: 2.8 % / Biso Wilson estimate: 33.27 Å2 / Rmerge(I) obs: 0.117 / Χ2: 3.633 / Net I/av σ(I): 15.212 / Net I/σ(I): 10.9 / Num. measured all: 41878
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.4-2.442.20.2586361.56283
2.44-2.492.30.2876821.47688.8
2.49-2.532.60.4067317.57693.7
2.53-2.592.80.2587561.33499.1
2.59-2.642.80.2347841.47799.5
2.64-2.72.80.2337442.04398.7
2.7-2.772.80.2177712.041100
2.77-2.852.80.1917752.65698.4
2.85-2.932.80.1687652.045100
2.93-3.022.80.1567461.93898.2
3.02-3.132.80.1267932.24799.6
3.13-3.262.80.1717517.62898.4
3.26-3.42.80.117663.84297.8
3.4-3.582.90.0977604.10999.3
3.58-3.812.90.0987745.14298.2
3.81-4.12.90.0827474.71997.9
4.1-4.512.80.0837745.52797.7
4.51-5.162.90.077614.42996.8
5.16-6.492.90.0817803.82397.5
6.49-302.80.0747805.80995.7

-
Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
BUSTER-TNT2.11.5refinement
PDB_EXTRACT3.14data extraction
RefinementResolution: 2.4→25.92 Å / Cor.coef. Fo:Fc: 0.9197 / Cor.coef. Fo:Fc free: 0.8801 / SU R Cruickshank DPI: 0.535 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.559 / SU Rfree Blow DPI: 0.264 / SU Rfree Cruickshank DPI: 0.267
RfactorNum. reflection% reflectionSelection details
Rfree0.2391 753 5 %RANDOM
Rwork0.1883 ---
obs0.1909 15072 96.55 %-
Displacement parametersBiso max: 119.2 Å2 / Biso mean: 26.6 Å2 / Biso min: 3.92 Å2
Baniso -1Baniso -2Baniso -3
1-0.275 Å20 Å2-6.0477 Å2
2---5.3514 Å20 Å2
3---5.0764 Å2
Refine analyzeLuzzati coordinate error obs: 0.278 Å
Refinement stepCycle: final / Resolution: 2.4→25.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2968 0 56 163 3187
Biso mean--23.3 29.08 -
Num. residues----368
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1096SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes96HARMONIC2
X-RAY DIFFRACTIONt_gen_planes442HARMONIC5
X-RAY DIFFRACTIONt_it3080HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion398SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3694SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d3080HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg4172HARMONIC21.13
X-RAY DIFFRACTIONt_omega_torsion3.05
X-RAY DIFFRACTIONt_other_torsion17.36
LS refinement shellResolution: 2.4→2.57 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.277 127 5.11 %
Rwork0.2254 2359 -
all0.2281 2486 -
obs--96.55 %
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)
11.5373-0.55360.5251.5607-0.11370.7646-0.1425-0.11010.11430.1706-0.0008-0.1601-0.0315-0.10650.1433-0.07330.0119-0.1051-0.1257-0.02170.05541.10651.518322.1631
20.57620.0420.29940.64010.06970.656-0.02390.02540.02090.0219-0.02920.0264-0.0507-0.01370.0531-0.07740.0009-0.076-0.07-0.0030.089312.3937-1.4472-4.3555
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|24 - A|230 }A24 - 230
2X-RAY DIFFRACTION2{ B|24 - B|230 }B24 - 230

+
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