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- PDB-7z9p: The novel DNA binding mechanism of ridinilazole, a precision Clos... -

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Basic information

Entry
Database: PDB / ID: 7z9p
TitleThe novel DNA binding mechanism of ridinilazole, a precision Clostridiodes difficile antibiotic
ComponentsDNA (5'-D(P*GP*CP*GP*AP*AP*TP*TP*CP*GP*CP*G*(RID))-3')
KeywordsDNA / Clostridiodes difficile / antibiotic / DNA-binding / drug discovery / target identification
Function / homologyRidinilazole / DNA / DNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsMason, S. / Leonard, P.M.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Antimicrob.Agents Chemother. / Year: 2023
Title: The Novel DNA Binding Mechanism of Ridinilazole, a Precision Clostridiodes difficile Antibiotic.
Authors: Mason, C.S. / Avis, T. / Hu, C. / Nagalingam, N. / Mudaliar, M. / Coward, C. / Begum, K. / Gajewski, K. / Alam, M.J. / Basseres, E. / Moss, S. / Reich, S. / Duperchy, E. / Fox, K.R. / Garey, K.W. / Powell, D.J.
History
DepositionMar 21, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 29, 2023Provider: repository / Type: Initial release
Revision 1.1May 3, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2May 31, 2023Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.3Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA (5'-D(P*GP*CP*GP*AP*AP*TP*TP*CP*GP*CP*G*(RID))-3')
B: DNA (5'-D(P*GP*CP*GP*AP*AP*TP*TP*CP*GP*CP*G*(RID))-3')
C: DNA (5'-D(P*GP*CP*GP*AP*AP*TP*TP*CP*GP*CP*G*(RID))-3')
D: DNA (5'-D(P*GP*CP*GP*AP*AP*TP*TP*CP*GP*CP*G*(RID))-3')
E: DNA (5'-D(P*GP*CP*GP*AP*AP*TP*TP*CP*GP*CP*G*(RID))-3')
F: DNA (5'-D(P*GP*CP*GP*AP*AP*TP*TP*CP*GP*CP*G*(RID))-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,84518
Polymers21,9806
Non-polymers1,86512
Water86548
1
A: DNA (5'-D(P*GP*CP*GP*AP*AP*TP*TP*CP*GP*CP*G*(RID))-3')
B: DNA (5'-D(P*GP*CP*GP*AP*AP*TP*TP*CP*GP*CP*G*(RID))-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,8345
Polymers7,3272
Non-polymers5073
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1530 Å2
ΔGint-36 kcal/mol
Surface area4200 Å2
MethodPISA
2
C: DNA (5'-D(P*GP*CP*GP*AP*AP*TP*TP*CP*GP*CP*G*(RID))-3')
D: DNA (5'-D(P*GP*CP*GP*AP*AP*TP*TP*CP*GP*CP*G*(RID))-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,1348
Polymers7,3272
Non-polymers8076
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1630 Å2
ΔGint-47 kcal/mol
Surface area4280 Å2
MethodPISA
3
E: DNA (5'-D(P*GP*CP*GP*AP*AP*TP*TP*CP*GP*CP*G*(RID))-3')
F: DNA (5'-D(P*GP*CP*GP*AP*AP*TP*TP*CP*GP*CP*G*(RID))-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,8775
Polymers7,3272
Non-polymers5503
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1620 Å2
ΔGint-46 kcal/mol
Surface area4320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.576, 40.320, 40.577
Angle α, β, γ (deg.)60.78, 87.31, 61.62
Int Tables number1
Space group name H-MP1

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Components

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DNA chain , 1 types, 6 molecules ABCDEF

#1: DNA chain
DNA (5'-D(P*GP*CP*GP*AP*AP*TP*TP*CP*GP*CP*G*(RID))-3')


Mass: 3663.392 Da / Num. of mol.: 6 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 5 types, 60 molecules

#2: Chemical ChemComp-IK7 / Ridinilazole / 2-pyridin-4-yl-5-(2-pyridin-4-yl-1H-benzimidazol-5-yl)-1H-benzimidazole


Mass: 388.424 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C24H16N6 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 48 / 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: 2.14 Å3/Da / Density % sol: 42.52 %
Crystal growTemperature: 287 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.01 M Zinc sulphate heptahydrate 0.1 M MES 6.5 25 % v/v PEG 500 MME

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Nov 26, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.2→30.08 Å / Num. obs: 8926 / % possible obs: 96.4 % / Redundancy: 1.7 % / CC1/2: 0.99 / Net I/σ(I): 5.3
Reflection shellResolution: 2.2→2.27 Å / Mean I/σ(I) obs: 1.1 / Num. unique obs: 725 / CC1/2: 0.548

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3U2N

3u2n


Resolution: 2.2→30.1 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.923 / SU B: 8.006 / SU ML: 0.207 / Cross valid method: THROUGHOUT / ESU R: 0.404 / ESU R Free: 0.231 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24137 410 4.6 %RANDOM
Rwork0.22373 ---
obs0.22485 8514 96.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 38.28 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å2-0.01 Å20.09 Å2
2---0.08 Å2-0.09 Å2
3----0.05 Å2
Refinement stepCycle: 1 / Resolution: 2.2→30.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1362 119 48 1529
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0121649
X-RAY DIFFRACTIONr_bond_other_d0.0020.017786
X-RAY DIFFRACTIONr_angle_refined_deg2.2661.7222520
X-RAY DIFFRACTIONr_angle_other_deg0.4011.5511848
X-RAY DIFFRACTIONr_dihedral_angle_1_deg
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1680.2258
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.02918
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02288
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.3963.9721649
X-RAY DIFFRACTIONr_scbond_other3.223.9561629
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.9265.9162491
X-RAY DIFFRACTIONr_long_range_B_refined5.4436.782424
X-RAY DIFFRACTIONr_long_range_B_other5.23136.5972405
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.325 9 -
Rwork0.252 608 -
obs--86.78 %

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