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- PDB-1s14: Crystal structure of Escherichia coli Topoisomerase IV ParE 24kDa... -

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Basic information

Entry
Database: PDB / ID: 1s14
TitleCrystal structure of Escherichia coli Topoisomerase IV ParE 24kDa subunit
ComponentsTopoisomerase IV subunit B
KeywordsISOMERASE / alpha/beta globular protein
Function / homology
Function and homology information


plasmid partitioning / DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) complex / sister chromatid cohesion / DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) activity / DNA topoisomerase (ATP-hydrolysing) / DNA topological change / chromosome organization / chromosome segregation / chromosome / response to antibiotic ...plasmid partitioning / DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) complex / sister chromatid cohesion / DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) activity / DNA topoisomerase (ATP-hydrolysing) / DNA topological change / chromosome organization / chromosome segregation / chromosome / response to antibiotic / DNA binding / ATP binding / metal ion binding / cytosol
Similarity search - Function
DNA topoisomerase IV, subunit B, Gram-negative / 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 IV, subunit B, Gram-negative / 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
NOVOBIOCIN / DNA topoisomerase 4 subunit B
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsWei, Y. / Gross, C.H.
CitationJournal: Antimicrob.Agents Chemother. / Year: 2004
Title: Crystal structures of Escherichia coli topoisomerase IV ParE subunit (24 and 43 kilodaltons): a single residue dictates differences in novobiocin potency against topoisomerase IV and DNA gyrase.
Authors: Bellon, S. / Parsons, J.D. / Wei, Y. / Hayakawa, K. / Swenson, L.L. / Charifson, P.S. / Lippke, J.A. / Aldape, R. / Gross, C.H.
History
DepositionJan 5, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 4, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Topoisomerase IV subunit B
B: Topoisomerase IV subunit B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,6824
Polymers43,4572
Non-polymers1,2252
Water9,476526
1
A: Topoisomerase IV subunit B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,3412
Polymers21,7281
Non-polymers6131
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Topoisomerase IV subunit B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,3412
Polymers21,7281
Non-polymers6131
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)74.900, 74.900, 138.200
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
DetailsTwo biological assemblies in the asymm. unit

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Components

#1: Protein Topoisomerase IV subunit B


Mass: 21728.393 Da / Num. of mol.: 2 / Fragment: 24kDa subunit
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: PARE, NFXD, B3030 / Production host: Escherichia coli (E. coli) / References: UniProt: P20083, EC: 5.99.1.-
#2: Chemical ChemComp-NOV / NOVOBIOCIN / 4-Hydroxy-3-[4-hydroxy-3-(3-methylbut-2-enyl)benzamido]-8-methylcoumarin-7-yl 3-O-carbamoyl-5,5-di-C-methyl-alpha-l-lyxofuranoside


Mass: 612.624 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C31H36N2O11 / Comment: antibiotic*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 526 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.57 Å3/Da / Density % sol: 52.21 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: 20% peg 3350, potassium tartrate, Sodium chloride, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 6, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / Num. obs: 30716 / % possible obs: 99.4 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Rsym value: 0.052
Reflection shellHighest resolution: 2 Å / Num. unique all: 176669 / Rsym value: 0.052 / % possible all: 99.4

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNXrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→20 Å / Cross valid method: THROUGHOUT / σ(F): 3 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.2788 15000 random
Rwork0.2191 --
obs0.2191 29580 -
all-30966 -
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2723 0 88 526 3337

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