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- PDB-6y8l: Mycobacterium thermoresistibile GyrB21 in complex with novobiocin -

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Basic information

Entry
Database: PDB / ID: 6y8l
TitleMycobacterium thermoresistibile GyrB21 in complex with novobiocin
ComponentsDNA gyrase subunit B
KeywordsDNA BINDING PROTEIN / Binding Sites / DNA Gyrase / inhibitors / novobiocin / topoisomerase 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, 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. ...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 / 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
NOVOBIOCIN / DNA gyrase subunit B / DNA gyrase subunit B
Similarity search - Component
Biological speciesMycolicibacterium thermoresistibile (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 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

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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)43,39912
Polymers41,6572
Non-polymers1,74210
Water5,260292
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5330 Å2
ΔGint-149 kcal/mol
Surface area15630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.962, 51.114, 83.205
Angle α, β, γ (deg.)90.000, 100.320, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: GLY / End label comp-ID: GLY / Refine code: _ / Auth seq-ID: 22 - 254 / Label seq-ID: 5 - 186

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

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Components

#1: Protein DNA gyrase subunit B


Mass: 20828.512 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycolicibacterium thermoresistibile (bacteria)
Gene: gyrB, RMCT_1109 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A117ILT2, UniProt: G7CIP8*PLUS, DNA topoisomerase (ATP-hydrolysing)
#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-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 292 / Source method: isolated from a natural source / Formula: H2O
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: 2.21 Å3/Da / Density % sol: 44.29 %
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 100 mM zinc chloride, 100 mM ammonium acetate, 3.5-5% (w/v) PEG6000, 3.5-5% (w/v) PEG8000, 3.5-5% (w/v) ...Details: Crystals grown with 17 mg/ml protein in the presence of 1 mM novobiocin against 100 mM zinc chloride, 100 mM ammonium acetate, 3.5-5% (w/v) PEG6000, 3.5-5% (w/v) PEG8000, 3.5-5% (w/v) PEG1000 and 100 mM Bis-Tris pH 7.0-7.3

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 12, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.4→81.86 Å / Num. obs: 71663 / % possible obs: 100 % / Redundancy: 6.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.048 / Rpim(I) all: 0.02 / Rrim(I) all: 0.052 / Net I/σ(I): 15.7 / Num. measured all: 463106 / Scaling rejects: 62
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
1.4-1.426.20.8752183735480.8490.380.9561.7100
7.67-81.866.30.03930114790.9980.0170.04354.399.7

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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: 1.4→81.86 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.964 / SU B: 2.627 / SU ML: 0.045 / SU R Cruickshank DPI: 0.0586 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.059 / ESU R Free: 0.057
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1813 3649 5.1 %RANDOM
Rwork0.1399 ---
obs0.142 67991 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 83.66 Å2 / Biso mean: 24.977 Å2 / Biso min: 14.1 Å2
Baniso -1Baniso -2Baniso -3
1-1.03 Å20 Å20.16 Å2
2---0.97 Å20 Å2
3----0.11 Å2
Refinement stepCycle: final / Resolution: 1.4→81.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2817 0 147 296 3260
Biso mean--28.31 37.82 -
Num. residues----363
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0133071
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172796
X-RAY DIFFRACTIONr_angle_refined_deg1.5131.6594184
X-RAY DIFFRACTIONr_angle_other_deg1.4321.5786427
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9695370
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.14420.651169
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.42715478
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.7971529
X-RAY DIFFRACTIONr_chiral_restr0.0770.2386
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023483
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02682
X-RAY DIFFRACTIONr_rigid_bond_restr2.57935867
Refine LS restraints NCS

Ens-ID: 1 / Number: 5531 / 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: 1.4→1.436 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.257 280 -
Rwork0.24 4988 -
all-5268 -
obs--99.96 %

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