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- PDB-6gav: Extremely 'open' clamp structure of DNA gyrase: role of the Coryn... -

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Basic information

Entry
Database: PDB / ID: 6gav
TitleExtremely 'open' clamp structure of DNA gyrase: role of the Corynebacteriales GyrB specific insert
ComponentsDNA gyrase subunit B,DNA gyrase subunit A
KeywordsDNA BINDING PROTEIN
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 / peptidoglycan-based cell wall / DNA-templated DNA replication / chromosome / response to antibiotic / magnesium ion binding ...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 / peptidoglycan-based cell wall / DNA-templated DNA replication / chromosome / response to antibiotic / magnesium ion binding / ATP hydrolysis activity / DNA binding / ATP binding / metal ion binding / plasma membrane / cytoplasm
Similarity search - Function
DNA gyrase, subunit A / DNA gyrase/topoisomerase IV, subunit A, C-terminal repeat / DNA gyrase/topoisomerase IV, subunit A, C-terminal / : / DNA gyrase C-terminal domain, beta-propeller / DNA gyrase subunit B, TOPRIM domain / DNA gyrase, subunit B / DNA topoisomerase, type IIA, subunit B / Histidine kinase/HSP90-like ATPase / DNA gyrase B subunit, C-terminal ...DNA gyrase, subunit A / DNA gyrase/topoisomerase IV, subunit A, C-terminal repeat / DNA gyrase/topoisomerase IV, subunit A, C-terminal / : / DNA gyrase C-terminal domain, beta-propeller / DNA gyrase subunit B, TOPRIM domain / DNA gyrase, subunit B / DNA topoisomerase, type IIA, subunit B / Histidine kinase/HSP90-like ATPase / DNA gyrase B subunit, C-terminal / DNA gyrase B subunit, carboxyl terminus / Topoisomerase (Topo) IIA-type catalytic domain profile. / DNA topoisomerase, type IIA, alpha-helical domain superfamily / DNA topoisomerase, type IIA, domain A / DNA topoisomerase, type IIA, domain A, alpha-beta / DNA gyrase/topoisomerase IV, subunit A / DNA Topoisomerase IV / 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-, DNA gyrase B-, and HSP90-like ATPase / Histidine kinase-like ATPases / Histidine kinase/HSP90-like ATPase superfamily / EF-hand calcium-binding domain. / Ribosomal protein S5 domain 2-type fold, subgroup / Ribosomal protein S5 domain 2-type fold
Similarity search - Domain/homology
DNA gyrase subunit B / DNA gyrase subunit A
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsPetrella, S. / Capton, E. / Alzari, P.M. / Aubry, A. / MAyer, C.
CitationJournal: Structure / Year: 2019
Title: Overall Structures of Mycobacterium tuberculosis DNA Gyrase Reveal the Role of a Corynebacteriales GyrB-Specific Insert in ATPase Activity.
Authors: Petrella, S. / Capton, E. / Raynal, B. / Giffard, C. / Thureau, A. / Bonnete, F. / Alzari, P.M. / Aubry, A. / Mayer, C.
History
DepositionApr 12, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 20, 2019Provider: repository / Type: Initial release
Revision 1.1Apr 10, 2019Group: Data collection / Database references / Category: citation / pdbx_database_proc
Item: _citation.journal_id_ISSN / _citation.journal_volume ..._citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)261,8757
Polymers260,8992
Non-polymers9765
Water84747
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11520 Å2
ΔGint20 kcal/mol
Surface area92840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.506, 157.617, 103.504
Angle α, β, γ (deg.)90.000, 98.110, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein DNA gyrase subunit B,DNA gyrase subunit A / Type IIA topoisomerase subunit GyrA


Mass: 130449.359 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: gyrB, gyrA, Rv0006, MTCY10H4.04 / Production host: Escherichia coli (E. coli) / References: UniProt: F6N7X0, UniProt: P9WG47, EC: 5.99.1.3
#2: Chemical
ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 47 / 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: 3.02 Å3/Da / Density % sol: 59.25 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop
Details: 100 mM Sodium Acetate 100 mM MES pH 6.5 26% PEG 400 25% EG 10 mM MgCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.987 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jul 11, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.6→46.15 Å / Num. obs: 94824 / % possible obs: 99.2 % / Redundancy: 3.38 % / Biso Wilson estimate: 74.91 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.104 / Net I/σ(I): 8.9
Reflection shellHighest resolution: 2.6 Å / Rmerge(I) obs: 1.253 / CC1/2: 0.531

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
XSCALEdata scaling
PDB_EXTRACT3.24data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3IFZ 3IG0 3ZKD

3ifz

3ig0

3zkd


Resolution: 2.6→46.15 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.905 / SU R Cruickshank DPI: 0.435 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.387 / SU Rfree Blow DPI: 0.257 / SU Rfree Cruickshank DPI: 0.269
RfactorNum. reflection% reflectionSelection details
Rfree0.24 4732 5.01 %RANDOM
Rwork0.197 ---
obs0.199 94491 99.5 %-
Displacement parametersBiso max: 235.61 Å2 / Biso mean: 94.53 Å2 / Biso min: 20 Å2
Baniso -1Baniso -2Baniso -3
1-13.9395 Å20 Å24.6896 Å2
2--21.8038 Å20 Å2
3----35.7432 Å2
Refine analyzeLuzzati coordinate error obs: 0.405 Å
Refinement stepCycle: final / Resolution: 2.6→46.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17437 0 60 47 17544
Biso mean--132.05 59.91 -
Num. residues----2236
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d6401SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes483HARMONIC2
X-RAY DIFFRACTIONt_gen_planes2587HARMONIC5
X-RAY DIFFRACTIONt_it17757HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion2337SEMIHARMONIC5
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_contact20148SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d17757HARMONIC20.008
X-RAY DIFFRACTIONt_angle_deg24018HARMONIC21.01
X-RAY DIFFRACTIONt_omega_torsion2.21
X-RAY DIFFRACTIONt_other_torsion19.71
LS refinement shellResolution: 2.6→2.67 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2507 317 4.54 %
Rwork0.2226 6673 -
all0.2239 6990 -
obs--99.2 %
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)
11.0558-0.24150.30710.3866-0.23360.8652-0.02380.1947-0.0532-0.10290.0007-0.08280.0008-0.15430.0231-0.1713-0.0030.0178-0.2378-0.1414-0.196380.1071-9.5464287.2821
20.5510.02060.00570.3799-0.28220.67470.0079-0.25220.12950.14350.0049-0.2564-0.06040.097-0.0128-0.24690.0151-0.1336-0.2096-0.12390.0623113.6223-10.6897329.7914
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }0
2X-RAY DIFFRACTION2{ B|* }0

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