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- PDB-1ei1: DIMERIZATION OF E. COLI DNA GYRASE B PROVIDES A STRUCTURAL MECHAN... -

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Basic information

Entry
Database: PDB / ID: 1ei1
TitleDIMERIZATION OF E. COLI DNA GYRASE B PROVIDES A STRUCTURAL MECHANISM FOR ACTIVATING THE ATPASE CATALYTIC CENTER
ComponentsDNA GYRASE B
KeywordsISOMERASE / ATPase domain / dimer
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 / cytosol / cytoplasm
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 / Ribosomal Protein S5; domain 2 - #10 / Toprim domain profile. / TOPRIM domain / Ribosomal Protein S5; domain 2 / 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
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / DNA gyrase subunit B / DNA gyrase subunit B
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.3 Å
AuthorsBrino, L. / Urzhumtsev, A. / Oudet, P. / Moras, D.
Citation
Journal: J.Biol.Chem. / Year: 2000
Title: Dimerization of Escherichia coli DNA-gyrase B provides a structural mechanism for activating the ATPase catalytic center.
Authors: Brino, L. / Urzhumtsev, A. / Mousli, M. / Bronner, C. / Mitschler, A. / Oudet, P. / Moras, D.
#1: Journal: Biochimie / Year: 1999
Title: Isoleucine 10 is Essential for DNA Gyrase B Function in Escherichia coli.
Authors: Brino, L. / Bronner, C. / Oudet, P. / Mousli, M.
#2: Journal: Plasmid / Year: 1997
Title: Expression in Escherichia coli of Y5-mutant and N-terminal Domain-deleted DNA Gyrase B Proteins Affects Strongly Plasmid Maintenance.
Authors: Brino, L. / Mousli, M. / Oudet, P. / Weiss, E.
History
DepositionFeb 23, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 31, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Feb 22, 2012Group: Structure summary
Revision 1.4Oct 4, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.5Nov 3, 2021Group: Database references / Derived calculations / Category: 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
Revision 1.6Feb 7, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA GYRASE B
B: DNA GYRASE B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,6529
Polymers86,1672
Non-polymers1,4857
Water9,098505
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8600 Å2
ΔGint-79 kcal/mol
Surface area29880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.7, 137.4, 78.9
Angle α, β, γ (deg.)90, 90, 90
Int Tables number18
Space group name H-MP21212
DetailsThe biological assembly is the dimer composed of chain A and B in the asymmetric unit.

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Components

#1: Protein DNA GYRASE B / GYRB


Mass: 43083.457 Da / Num. of mol.: 2 / Fragment: N-TERMINAL 43 KDA FRAGMENT / Mutation: Y5S, Y405S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli)
Description: PN43-Y5S (TAC PROMOTER, BETA LACTAMASE GENE, LAC IQ GENE, PBR322 BACKGROUND)
Plasmid: PTTQ18 VECTOR(PAG111; PN43-Y5S) / Production host: Escherichia coli (E. coli)
References: UniProt: P06982, UniProt: P0AES6*PLUS, EC: 5.99.1.3
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 505 / 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: 2.66 Å3/Da / Density % sol: 53.82 %
Crystal growTemperature: 279 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG400, ammonium sulfate, ADPNP, HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 279K
Crystal grow
*PLUS
Temperature: 4 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
1100 mMHEPES1reservoirpH7.5
24 %PEG4001reservoir
30.2 Mammonium sulfate1reservoir
420 mg/mlprotein1drop
510 mMADPNP1drop

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: LURE / Beamline: DW32 / Wavelength: 0.91
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91 Å / Relative weight: 1
ReflectionResolution: 2.3→15 Å / Num. obs: 33856 / % possible obs: 80 % / Observed criterion σ(F): 3 / Redundancy: 3.4 % / Rmerge(I) obs: 0.044 / Net I/σ(I): 26.4
Reflection shellResolution: 2.3→2.5 Å / Num. unique all: 33856 / % possible all: 56
Reflection
*PLUS
Num. measured all: 114762
Reflection shell
*PLUS
% possible obs: 56 %

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Processing

Software
NameVersionClassification
AMoREphasing
X-PLOR3.1refinement
XDSdata reduction
AUTOMARdata reduction
RefinementResolution: 2.3→6 Å / σ(F): 2 / Stereochemistry target values: XPLOR standard
RfactorNum. reflection% reflectionSelection details
Rfree0.266 2579 -random
Rwork0.166 ---
obs-25481 65.1 %-
Refinement stepCycle: LAST / Resolution: 2.3→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6056 0 89 505 6650
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_deg1.6
X-RAY DIFFRACTIONx_bond_d0.008
X-RAY DIFFRACTIONx_torsion_impr_deg3.3
X-RAY DIFFRACTIONx_dihedral_deg25
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 6 Å / σ(F): 2 / Rfactor obs: 0.171
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_deg1.6
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg25
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg3.3

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