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- PDB-9h2z: Crystal structure of APH(2")-IVa alternate (soaking with EK3-18 i... -

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Basic information

Entry
Database: PDB / ID: 9h2z
TitleCrystal structure of APH(2")-IVa alternate (soaking with EK3-18 inhibitor)
ComponentsAPH(2'')-Id
KeywordsTRANSFERASE / Aminoglycoside phosphotransferase / kinase / soluble protein / antibiotic resistance
Function / homology: / Aminoglycoside phosphotransferase / Phosphotransferase enzyme family / nucleotide binding / Protein kinase-like domain superfamily / metal ion binding / APH(2'')-Id
Function and homology information
Biological speciesEnterococcus casseliflavus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsKaplan, E. / Guichou, J.-F. / Gelin, M. / Chaloin, L. / Lionne, C.
Funding support France, 1items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR)ANR-19-AMRB-0001 France
CitationJournal: Chemmedchem / Year: 2025
Title: APH Inhibitors that Reverse Aminoglycoside Resistance in Enterococcus casseliflavus.
Authors: Kaplan, E. / Chaloin, L. / Guichou, J.F. / Berrou, K. / Rahimova, R. / Labesse, G. / Lionne, C.
History
DepositionOct 15, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 5, 2025Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2025Group: Database references / Category: citation / Item: _citation.journal_volume

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: APH(2'')-Id
B: APH(2'')-Id


Theoretical massNumber of molelcules
Total (without water)75,1942
Polymers75,1942
Non-polymers00
Water86548
1
A: APH(2'')-Id


Theoretical massNumber of molelcules
Total (without water)37,5971
Polymers37,5971
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: APH(2'')-Id


Theoretical massNumber of molelcules
Total (without water)37,5971
Polymers37,5971
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.490, 63.010, 87.218
Angle α, β, γ (deg.)90.00, 92.74, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein APH(2'')-Id


Mass: 37596.770 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterococcus casseliflavus (bacteria) / Gene: aph(2'')-Id / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O68183
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 48 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 291.15 K / Method: vapor diffusion, hanging drop / Details: 10% PEG3350, 50 mM Ammonium Citrate pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.966 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Jul 19, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.966 Å / Relative weight: 1
ReflectionResolution: 2.4→63.01 Å / Num. obs: 25362 / % possible obs: 98 % / Redundancy: 3.2 % / CC1/2: 0.99 / Rmerge(I) obs: 0.073 / Net I/σ(I): 7.7
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 3 % / Rmerge(I) obs: 0.451 / Num. unique obs: 2675 / CC1/2: 0.743

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
Aimlessdata scaling
PHASERphasing
autoPROCdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→60.49 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.888 / SU B: 12.724 / SU ML: 0.281 / Cross valid method: THROUGHOUT / ESU R: 0.568 / ESU R Free: 0.327 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29169 1231 4.9 %RANDOM
Rwork0.20782 ---
obs0.21162 24025 97.57 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 50.777 Å2
Baniso -1Baniso -2Baniso -3
1-0.82 Å20 Å20.89 Å2
2---2.98 Å2-0 Å2
3---2.07 Å2
Refinement stepCycle: 1 / Resolution: 2.4→60.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4947 0 0 48 4995
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0125065
X-RAY DIFFRACTIONr_bond_other_d0.0010.0164759
X-RAY DIFFRACTIONr_angle_refined_deg1.4351.8426825
X-RAY DIFFRACTIONr_angle_other_deg0.5071.78311029
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.395595
X-RAY DIFFRACTIONr_dihedral_angle_2_deg12.313520
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.41510946
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.070.2721
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.025803
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021157
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_it3.7744.7662386
X-RAY DIFFRACTIONr_mcbond_other3.774.7672386
X-RAY DIFFRACTIONr_mcangle_it5.8148.5582979
X-RAY DIFFRACTIONr_mcangle_other5.8138.562980
X-RAY DIFFRACTIONr_scbond_it4.4375.3742679
X-RAY DIFFRACTIONr_scbond_other4.4375.3752680
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.2489.623847
X-RAY DIFFRACTIONr_long_range_B_refined9.48850.285691
X-RAY DIFFRACTIONr_long_range_B_other9.48750.295690
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.354 102 -
Rwork0.269 1792 -
obs--99.53 %

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