[English] 日本語
Yorodumi
- PDB-5yig: Crystal structure of Streptococcus pneumonia ParE with inhibitor -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5yig
TitleCrystal structure of Streptococcus pneumonia ParE with inhibitor
ComponentsDNA topoisomerase 4 subunit BTopoisomerase
KeywordsANTIMICROBIAL PROTEIN / Inhibitor
Function / homology
Function and homology information


DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) activity / DNA topoisomerase (ATP-hydrolysing) / DNA topological change / chromosome segregation / chromosome / DNA binding / ATP binding
Similarity search - Function
DNA topoisomerase 4 subunit B, Firmicutes/Mollicutes / 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 ...DNA topoisomerase 4 subunit B, Firmicutes/Mollicutes / 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-54B / DNA topoisomerase 4 subunit B
Similarity search - Component
Biological speciesStreptococcus pneumoniae GA47502 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.8 Å
AuthorsCherian, J. / Tan, Y. / Hill, J.
Funding support Singapore, 1items
OrganizationGrant numberCountry
Astar Singapore
CitationJournal: Eur J Med Chem / Year: 2018
Title: Discovery of dual GyrB/ParE inhibitors active against Gram-negative bacteria.
Authors: Ho, S.Y. / Wang, W. / Ng, F.M. / Wong, Y.X. / Poh, Z.Y. / Tan, S.W.E. / Ang, S.H. / Liew, S.S. / Joyner Wong, Y.S. / Tan, Y. / Poulsen, A. / Pendharkar, V. / Sangthongpitag, K. / Manchester, ...Authors: Ho, S.Y. / Wang, W. / Ng, F.M. / Wong, Y.X. / Poh, Z.Y. / Tan, S.W.E. / Ang, S.H. / Liew, S.S. / Joyner Wong, Y.S. / Tan, Y. / Poulsen, A. / Pendharkar, V. / Sangthongpitag, K. / Manchester, J. / Basarab, G. / Hill, J. / Keller, T.H. / Cherian, J.
History
DepositionOct 4, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 5, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_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_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: DNA topoisomerase 4 subunit B
B: DNA topoisomerase 4 subunit B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,6734
Polymers45,4692
Non-polymers1,2032
Water1086
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area470 Å2
ΔGint-1 kcal/mol
Surface area18480 Å2
Unit cell
Length a, b, c (Å)43.394, 61.980, 84.824
Angle α, β, γ (deg.)90.000, 99.030, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / End auth comp-ID: ASN / End label comp-ID: ASN

Dom-IDBeg auth comp-IDBeg label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1VALVALchain AAA18 - 2262 - 210
2GLNGLNchain BBB17 - 2261 - 210

-
Components

#1: Protein DNA topoisomerase 4 subunit B / Topoisomerase / Topoisomerase IV subunit B


Mass: 22734.660 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae GA47502 (bacteria)
Gene: parE, SPAR98_0871 / Production host: Escherichia coli K-12 (bacteria) / Strain (production host): K-12 / References: UniProt: G6JAH7, EC: 5.99.1.3
#2: Chemical ChemComp-54B / 1-ethyl-3-[5-[2-[(1S,5R)-3-methyl-3,8-diazabicyclo[3.2.1]octan-8-yl]-5-(2-oxidanylidene-3H-1,3,4-oxadiazol-5-yl)pyridin-3-yl]-4-[4-(trifluoromethyl)-1,3-thiazol-2-yl]pyridin-2-yl]urea


Mass: 601.603 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C26H26F3N9O3S
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 6 / 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: 2.66 Å3/Da / Density % sol: 53.71 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 0.2M Sodium Acetate, 18-22% PEG 3350

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.54 Å
DetectorType: RIGAKU AFC-5R / Detector: CCD / Date: Oct 17, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.8→35.934 Å / Num. obs: 21230 / % possible obs: 99.51 % / Redundancy: 2.8 % / Biso Wilson estimate: 30.41 Å2 / Rmerge(I) obs: 0.179 / Net I/σ(I): 5.72
Reflection shellResolution: 1.8001→2.8652 Å

-
Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.8 Å35.93 Å
Translation2.8 Å35.93 Å

-
Processing

Software
NameVersionClassification
SAINTV8.34Adata scaling
PHASER2.5.6phasing
PHENIX1.9_1692refinement
PDB_EXTRACT3.15data extraction
d*TREKdata collection
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→35.934 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.63
Details: THE STRUCTURE FACTOR FILE CONTAINS FRIEDEL PAIRS IN I_PLUS/MINUS COLUMNS
RfactorNum. reflection% reflection
Rfree0.2552 2119 9.98 %
Rwork0.2059 --
obs0.2108 21230 98.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 93.82 Å2 / Biso mean: 25.6232 Å2 / Biso min: 4.84 Å2
Refinement stepCycle: final / Resolution: 2.8→35.934 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2961 0 84 6 3051
Biso mean--29.17 16.06 -
Num. residues----386
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053185
X-RAY DIFFRACTIONf_angle_d0.9914338
X-RAY DIFFRACTIONf_chiral_restr0.03495
X-RAY DIFFRACTIONf_plane_restr0.005552
X-RAY DIFFRACTIONf_dihedral_angle_d14.3481232
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1694X-RAY DIFFRACTION2.993TORSIONAL
12B1694X-RAY DIFFRACTION2.993TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.8001-2.86520.29171430.23431272141599
2.8652-2.93680.32681390.260712951434100
2.9368-3.01620.36161460.2511288143499
3.0162-3.10490.3291430.25751282142599
3.1049-3.20510.2841370.25951259139699
3.2051-3.31950.29421410.25081281142299
3.3195-3.45230.33191420.24471278142099
3.4523-3.60930.24711400.24021293143398
3.6093-3.79940.26741340.22911206134097
3.7994-4.03720.24641400.18811283142399
4.0372-4.34840.21341410.17631289143099
4.3484-4.78510.19691460.14661290143699
4.7851-5.47540.20891410.154512751416100
5.4754-6.89040.231480.172512941442100
6.8904-35.93670.19551380.17281226136496

+
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