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- PDB-6y8o: Mycobacterium smegmatis GyrB 22kDa ATPase sub-domain in complex w... -

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Basic information

Entry
Database: PDB / ID: 6y8o
TitleMycobacterium smegmatis GyrB 22kDa ATPase sub-domain in complex with novobiocin
ComponentsDNA gyrase subunit B
KeywordsDNA BINDING PROTEIN / Binding Sites / DNA Gyrase / inhibitors / / novobiocin IV / ISOMERASE
Function / homology
Function and homology information


DNA negative supercoiling activity / DNA topoisomerase (ATP-hydrolysing) / DNA topological change / DNA-templated DNA replication / chromosome / DNA binding / ATP binding / metal ion binding / cytoplasm
Similarity search - Function
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 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 / Toprim domain profile. / TOPRIM domain / 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
Similarity search - Domain/homology
ACETATE ION / NOVOBIOCIN / DNA gyrase subunit B / DNA gyrase subunit B
Similarity search - Component
Biological speciesMycolicibacterium smegmatis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsHenderson, S.R. / Stevenson, C.E.M. / Malone, B. / Zholnerovych, Y. / Mitchenall, L.A. / Pichowicz, M. / McGarry, D.H. / Cooper, I.R. / Charrier, C. / Salisbury, A. ...Henderson, S.R. / Stevenson, C.E.M. / Malone, B. / Zholnerovych, Y. / Mitchenall, L.A. / Pichowicz, M. / McGarry, D.H. / Cooper, I.R. / Charrier, C. / Salisbury, A. / Lawson, D.M. / Maxwell, A.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/P012523/1 United Kingdom
Wellcome Trust110072/Z/15/Z United Kingdom
CitationJournal: J.Antimicrob.Chemother. / Year: 2020
Title: Structural and mechanistic analysis of ATPase inhibitors targeting mycobacterial DNA gyrase.
Authors: Henderson, S.R. / Stevenson, C.E.M. / Malone, B. / Zholnerovych, Y. / Mitchenall, L.A. / Pichowicz, M. / McGarry, D.H. / Cooper, I.R. / Charrier, C. / Salisbury, A.M. / Lawson, D.M. / Maxwell, A.
History
DepositionMar 5, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 12, 2020Provider: repository / Type: Initial release
Revision 1.1Sep 30, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 24, 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 / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)54,44322
Polymers52,3042
Non-polymers2,13820
Water6,810378
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5760 Å2
ΔGint-10 kcal/mol
Surface area17380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)156.962, 56.112, 50.678
Angle α, β, γ (deg.)90.000, 90.660, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: THR / Beg label comp-ID: THR / End auth comp-ID: PRO / End label comp-ID: PRO / Refine code: _ / Auth seq-ID: 18 - 254 / Label seq-ID: 29 - 233

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein DNA gyrase subunit B


Mass: 26152.248 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycolicibacterium smegmatis (bacteria) / Gene: gyrB / Production host: Escherichia coli (E. coli)
References: UniProt: P0C559, UniProt: A0QNE0*PLUS, DNA topoisomerase (ATP-hydrolysing)

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Non-polymers , 5 types, 398 molecules

#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 / Feature type: SUBJECT OF INVESTIGATION / Comment: antibiotic*YM
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 378 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.31 Å3/Da / Density % sol: 46.66 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: Crystals grown with 17 mg/ml protein in the presence of 1 mM novobiocin against 15% (w/v) PEG8000, 100 mM sodium acetate pH 5.6, 200 mM calcium acetate were harvested in the precipitant ...Details: Crystals grown with 17 mg/ml protein in the presence of 1 mM novobiocin against 15% (w/v) PEG8000, 100 mM sodium acetate pH 5.6, 200 mM calcium acetate were harvested in the precipitant supplemented with 25% (v/v) ethylene glycol for cryoprotection.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9159 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 9, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9159 Å / Relative weight: 1
ReflectionResolution: 1.6→78.48 Å / Num. obs: 58273 / % possible obs: 100 % / Redundancy: 6.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.11 / Rpim(I) all: 0.046 / Rrim(I) all: 0.119 / Net I/σ(I): 10.4 / Num. measured all: 387422 / Scaling rejects: 148
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.6-1.636.81.0711927528530.6470.441.1592100
8.76-78.486.90.024268138810.010.02647.699.9

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Processing

Software
NameVersionClassification
Aimless0.7.4data scaling
REFMAC5.8.0258refinement
PDB_EXTRACT3.25data extraction
DIALSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4B6C

4b6c


Resolution: 1.6→78.48 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.965 / SU B: 4.628 / SU ML: 0.067 / SU R Cruickshank DPI: 0.0873 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.087 / ESU R Free: 0.078
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.188 2973 5.1 %RANDOM
Rwork0.134 ---
obs0.1367 55300 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 81.5 Å2 / Biso mean: 21.903 Å2 / Biso min: 9.86 Å2
Baniso -1Baniso -2Baniso -3
1--1.78 Å20 Å2-0.27 Å2
2--0.39 Å20 Å2
3---1.4 Å2
Refinement stepCycle: final / Resolution: 1.6→78.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2931 0 141 389 3461
Biso mean--26.74 35.39 -
Num. residues----374
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0133303
X-RAY DIFFRACTIONr_bond_other_d0.0020.0173021
X-RAY DIFFRACTIONr_angle_refined_deg1.5141.6634486
X-RAY DIFFRACTIONr_angle_other_deg1.4281.5796954
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0155407
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.33120.632190
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.13115536
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.1541533
X-RAY DIFFRACTIONr_chiral_restr0.0760.2415
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023819
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02750
X-RAY DIFFRACTIONr_rigid_bond_restr2.67236324
Refine LS restraints NCS

Ens-ID: 1 / Number: 6058 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.11 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.6→1.642 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.31 214 -
Rwork0.26 4085 -
all-4299 -
obs--99.86 %

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