[English] 日本語
Yorodumi
- PDB-9gef: Experimental localization of metal-binding sites reveals the role... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9gef
TitleExperimental localization of metal-binding sites reveals the role of metal ions in the delafloxacin-stabilized Streptococcus pneumoniae topoisomerase IV DNA cleavage complex
Components
  • DNA (5'-D(*GP*TP*AP*AP*TP*AP*C)-3')
  • DNA (5'-D(*TP*GP*TP*GP*GP*AP*T)-3')
  • DNA (5'-D(P*AP*AP*CP*CP*GP*TP*AP*TP*TP*AP*C)-3')
  • DNA (5'-D(P*GP*GP*TP*TP*AP*TP*CP*CP*AP*CP*A)-3')
  • DNA TOPOISOMERASE (ATP-HYDROLYZING),DNA TOPOISOMERASE 4
KeywordsDNA BINDING PROTEIN / metal ions / Type II topoisomerases / Fluoroquinolones / Long-wavelength X-ray crystallography
Function / homologyACETATE ION / : / delafloxacin / DNA / DNA (> 10)
Function and homology information
Biological speciesStreptococcus pneumoniae (bacteria)
Escherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.62 Å
AuthorsWang, B. / Najmudin, S. / Pan, X.-S. / Mykhaylyk, V. / Orr, C. / Wagner, A. / Govada, L. / Chayen, N.E. / Fisher, L.M. / Sanderson, M.R.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Other governmentMR/T000848 United Kingdom
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2024
Title: Experimental localization of metal-binding sites reveals the role of metal ions in type II DNA topoisomerases.
Authors: Wang, B. / Najmudin, S. / Pan, X.S. / Mykhaylyk, V. / Orr, C. / Wagner, A. / Govada, L. / Chayen, N.E. / Fisher, L.M. / Sanderson, M.R.
History
DepositionAug 8, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 16, 2024Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: DNA TOPOISOMERASE (ATP-HYDROLYZING),DNA TOPOISOMERASE 4
B: DNA TOPOISOMERASE (ATP-HYDROLYZING),DNA TOPOISOMERASE 4
E: DNA (5'-D(*TP*GP*TP*GP*GP*AP*T)-3')
F: DNA (5'-D(P*GP*GP*TP*TP*AP*TP*CP*CP*AP*CP*A)-3')
G: DNA (5'-D(*GP*TP*AP*AP*TP*AP*C)-3')
H: DNA (5'-D(P*AP*AP*CP*CP*GP*TP*AP*TP*TP*AP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)176,70427
Polymers174,8106
Non-polymers1,89421
Water1,946108
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20380 Å2
ΔGint-171 kcal/mol
Surface area61690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)158.533, 158.533, 210.820
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein DNA TOPOISOMERASE (ATP-HYDROLYZING),DNA TOPOISOMERASE 4


Mass: 81934.758 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: THE FUSED TOPOISOMERASE IV CLEAVAGE COMPLEX COMPRISES THE C-TERMINAL DOMAIN OF THE PARE30 DOMAIN (RESIDUES 415-647), A HIS INSERT AT POSITION 648 AND THE N-TERMINAL DOMAIN OF PARC55 (RESIDUES 1001-1486),
Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Strain: 7785 / Gene: AMCSP13_000989, PARC, SP_0855 / Plasmid: PET29A / Production host: Escherichia coli (E. coli) / References: DNA topoisomerase (ATP-hydrolysing)

-
DNA chain , 4 types, 4 molecules EFGH

#2: DNA chain DNA (5'-D(*TP*GP*TP*GP*GP*AP*T)-3')


Mass: 2168.445 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: PLAMID PBR322 / Source: (synth.) Escherichia coli (E. coli)
#3: DNA chain DNA (5'-D(P*GP*GP*TP*TP*AP*TP*CP*CP*AP*CP*A)-3')


Mass: 3333.198 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: PLASMID PBR322 / Source: (synth.) Escherichia coli (E. coli)
#4: DNA chain DNA (5'-D(*GP*TP*AP*AP*TP*AP*C)-3')


Mass: 2121.436 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: PLAMID PBR322 / Source: (synth.) Escherichia coli (E. coli)
#5: DNA chain DNA (5'-D(P*AP*AP*CP*CP*GP*TP*AP*TP*TP*AP*C)-3')


Mass: 3317.199 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: PLAMID PBR322 / Source: (synth.) Escherichia coli (E. coli)

-
Non-polymers , 7 types, 129 molecules

#6: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#7: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#8: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: K
#9: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#10: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#11: Chemical ChemComp-TE9 / delafloxacin / 1-[6-azanyl-3,5-bis(fluoranyl)pyridin-2-yl]-8-chloranyl-6-fluoranyl-7-(3-oxidanylazetidin-1-yl)-4-oxidanylidene-quinoline-3-carboxylic acid


Mass: 440.760 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H12ClF3N4O4
#12: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 108 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestN
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 4.37 Å3/Da / Density % sol: 71.88 % / Description: rod-shaped
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 50 mM sodium cacodylate, 62.5 mM KCl, 7.5 mM MgCl 2 , 2.5% Tacsimate TM Hampton Research, 5.5-7% isopropanol, pH 6.5. The protein crystals were cryoprotected with 50 mM sodium cacodylate pH ...Details: 50 mM sodium cacodylate, 62.5 mM KCl, 7.5 mM MgCl 2 , 2.5% Tacsimate TM Hampton Research, 5.5-7% isopropanol, pH 6.5. The protein crystals were cryoprotected with 50 mM sodium cacodylate pH 6.5, 62.5 mM KCl, 7.5 mM MgCl 2 , 2.5% Tacsimate TM Hampton Research, 1 mM beta-mercaptoethanol and 30% v/v MPD before being flash-cooled in liquid nitrogen and collected in elliptical polyimide sample mounts.
PH range: 6.5 - 8.0

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I23 / Wavelength: 2.75, 3.14, 3.54, 4.35, 4.50 and 5.16
DetectorType: DECTRIS PILATUS 12M / Detector: PIXEL / Date: Sep 23, 2023
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
12.751
23.141
33.541
44.351
54.51
65.161
ReflectionResolution: 2.37→210.82 Å / Num. obs: 124385 / % possible obs: 100 % / Redundancy: 59.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.215 / Rpim(I) all: 0.027 / Net I/σ(I): 11.6
Reflection shellResolution: 2.37→2.41 Å / Redundancy: 45 % / Rmerge(I) obs: 5.369 / Num. unique obs: 6112 / CC1/2: 0.204 / Rpim(I) all: 0.796 / % possible all: 100

-
Processing

Software
NameVersionClassification
PDB-REDO8.11refinement
PHENIX4.4.7refinement
DIALSdata reduction
xia2.multiplexdata scaling
DIMPLEphasing
STARANISOdata scaling
CootAfter using ANODEmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.62→79.39 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.926 / SU B: 26.622 / SU ML: 0.23 / Cross valid method: THROUGHOUT / ESU R: 0.524 / ESU R Free: 0.276 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2085 1109 1.7 %RANDOM
Rwork0.18041 ---
obs0.18089 62910 69.46 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å / Solvent model: MASK
Displacement parametersBiso mean: 48.179 Å2
Baniso -1Baniso -2Baniso -3
1--1.27 Å2-0.63 Å2-0 Å2
2---1.27 Å20 Å2
3---4.11 Å2
Refinement stepCycle: LAST / Resolution: 2.62→79.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11504 732 110 108 12454
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.01712671
X-RAY DIFFRACTIONr_bond_other_d0.0010.01611900
X-RAY DIFFRACTIONr_angle_refined_deg1.441.79617211
X-RAY DIFFRACTIONr_angle_other_deg0.4551.56927449
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3595.2931534
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.274206
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.526102216
X-RAY DIFFRACTIONr_chiral_restr0.0610.21918
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0214178
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022726
X-RAY DIFFRACTIONr_mcbond_it1.5641.895783
X-RAY DIFFRACTIONr_mcbond_other1.5641.8895782
X-RAY DIFFRACTIONr_mcangle_it2.7183.3967236
X-RAY DIFFRACTIONr_mcangle_other2.7163.3947225
X-RAY DIFFRACTIONr_scbond_it2.0221.9096888
X-RAY DIFFRACTIONr_scbond_other2.0221.9096889
X-RAY DIFFRACTIONr_scangle_other2.8833.4259978
X-RAY DIFFRACTIONr_long_range_B_refined5.66217.7416097
X-RAY DIFFRACTIONr_long_range_B_other5.66217.7516094
LS refinement shellResolution: 2.622→2.69 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.117 3 -
Rwork0.348 359 -
obs--5.35 %
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)
11.09850.54230.01820.53340.03580.57460.00950.0303-0.16270.02620.0336-0.15130.05850.3033-0.04310.28740.02580.00290.3283-0.03820.0463-48.21560.882-36.312
21.15630.48910.090.53510.10020.43310.059-0.0450.24860.0172-0.02610.0751-0.29010.0126-0.03290.32380.00950.04020.2634-0.02360.0621-54.51367.731-0.033
37.7024-7.1735-0.465311.31531.29150.19440.0097-0.41281.1660.0281-0.086-0.3181-0.015-0.00750.07630.3223-0.1298-0.01750.4751-0.10020.3083-38.02470.336-35.605
45.32380.2692-1.19680.17930.12460.47650.24410.14041.2321-0.320.1618-0.0434-0.42270.1712-0.40590.7673-0.14870.29770.5603-0.01960.3603-33.77972.105-32.236
52.6509-2.3032-0.322611.04612.47650.59450.02350.4074-0.42750.13390.2653-1.14050.0230.2041-0.28880.233-0.0371-0.02960.5905-0.04360.355-41.472.8950.698
64.04911.4821-0.7652.87271.34441.27830.2033-0.3427-0.09360.15650.506-1.08410.02730.5242-0.70920.59350.1212-0.03230.5161-0.22340.484-37.98676.14-2.471
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A411 - 1485
2X-RAY DIFFRACTION2B411 - 1485
3X-RAY DIFFRACTION3E9 - 15
4X-RAY DIFFRACTION4F1 - 11
5X-RAY DIFFRACTION5G9 - 15
6X-RAY DIFFRACTION6H1 - 11

+
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