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- PDB-6y8n: Mycobacterium thermoresistibile GyrB21 in complex with Redx03863 -

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Basic information

Entry
Database: PDB / ID: 6y8n
TitleMycobacterium thermoresistibile GyrB21 in complex with Redx03863
ComponentsDNA gyrase subunit B
KeywordsDNA BINDING PROTEIN / Binding Sites / DNA Gyrase / inhibitors / / Redx03863 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
Chem-OGH / DNA gyrase subunit B / DNA gyrase subunit B
Similarity search - Component
Biological speciesMycolicibacterium thermoresistibile (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 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)43,01512
Polymers41,6572
Non-polymers1,35710
Water5,206289
1
A: DNA gyrase subunit B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,5697
Polymers20,8291
Non-polymers7416
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: DNA gyrase subunit B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,4455
Polymers20,8291
Non-polymers6174
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)43.769, 51.666, 82.911
Angle α, β, γ (deg.)90.000, 100.250, 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: PRO / End label comp-ID: PRO / Refine code: _ / Auth seq-ID: 22 - 253 / Label seq-ID: 5 - 185

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-OGH / 4-[(1~{S},5~{R})-6-azanyl-3-azabicyclo[3.1.0]hexan-3-yl]-6-fluoranyl-~{N}-methyl-2-(2-methylpyrimidin-5-yl)oxy-9~{H}-pyrimido[4,5-b]indol-8-amine


Mass: 420.443 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H21FN8O / Feature type: SUBJECT OF INVESTIGATION
#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.: 289 / 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: 44.46 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 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
PH range: 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: 1.5→51.67 Å / Num. obs: 58503 / % possible obs: 100 % / Redundancy: 6.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.062 / Rpim(I) all: 0.026 / Rrim(I) all: 0.067 / Net I/σ(I): 12.5 / Num. measured all: 374604 / Scaling rejects: 116
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
1.5-1.536.31.4551817028630.6790.6261.5881.299.9
8.22-51.676.20.03524713970.9990.0150.03843.899.6

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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: 1.5→43.69 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.965 / SU B: 4.08 / SU ML: 0.064 / SU R Cruickshank DPI: 0.0787 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.079 / ESU R Free: 0.074
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2027 2826 4.8 %RANDOM
Rwork0.1489 ---
obs0.1515 55659 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 77.08 Å2 / Biso mean: 25.059 Å2 / Biso min: 15.3 Å2
Baniso -1Baniso -2Baniso -3
1-0.24 Å20 Å2-0.42 Å2
2--0.17 Å20 Å2
3----0.23 Å2
Refinement stepCycle: final / Resolution: 1.5→43.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2785 0 76 296 3157
Biso mean--26.65 38.3 -
Num. residues----360
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0132982
X-RAY DIFFRACTIONr_bond_other_d0.0020.0172692
X-RAY DIFFRACTIONr_angle_refined_deg1.6591.6544066
X-RAY DIFFRACTIONr_angle_other_deg1.4661.5796197
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0985370
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.1621.138167
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.60315463
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.2331527
X-RAY DIFFRACTIONr_chiral_restr0.0750.2381
X-RAY DIFFRACTIONr_gen_planes_refined0.010.023420
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02665
X-RAY DIFFRACTIONr_rigid_bond_restr2.81735674
Refine LS restraints NCS

Ens-ID: 1 / Number: 5498 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.1 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.5→1.539 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.32 208 -
Rwork0.278 4079 -
all-4287 -
obs--99.86 %

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