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- PDB-9qoe: APH(2'')-Id with a fragment -

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Basic information

Entry
Database: PDB / ID: 9qoe
TitleAPH(2'')-Id with a fragment
ComponentsAPH(2'')-Id
KeywordsANTIBIOTIC / inhibitor / complex / enzyme
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: 2.3 Å
AuthorsGuichou, J.F. / Gelin, M. / Tomaszczyk, M. / Kowalewski, J. / Lionne, C.
Funding support France, 3items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR)ANR-19-AMRB-0001 France
Agence Nationale de la Recherche (ANR)(ANR-10-INBS-0004 France
Agence Nationale de la Recherche (ANR)(ANR-10-INBS-0005 France
CitationJournal: Commun Chem / Year: 2025
Title: Fragment-based drug design of a bacterial kinase inhibitor capable of increasing the antibiotic sensitivity of clinical isolates.
Authors: Kowalewski, J. / Deutscher, R. / Richardoz, M. / Tomaszczyk, M. / Gelin, M. / Labesse, G. / Hausch, F. / Wright, G.D. / Dunyach-Remy, C. / Guichou, J.F. / Lionne, C.
History
DepositionMar 26, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 11, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)75,6975
Polymers75,1942
Non-polymers5033
Water1,47782
1
A: APH(2'')-Id
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,8883
Polymers37,5971
Non-polymers2912
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: APH(2'')-Id
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,8092
Polymers37,5971
Non-polymers2131
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)76.170, 65.580, 78.060
Angle α, β, γ (deg.)90.00, 92.13, 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 (E. coli) / References: UniProt: O68183
#2: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#3: Chemical ChemComp-A1I77 / 5-chloranyl-2-(cyclopropylamino)pyridine-4-carboxylic acid


Mass: 212.633 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H9ClN2O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 82 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.59 Å3/Da / Density % sol: 52.53 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 12% PEG3350, 50-90 mM Ammonium citrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.9897 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 27, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9897 Å / Relative weight: 1
ReflectionResolution: 2.3→42.37 Å / Num. obs: 33996 / % possible obs: 98.52 % / Redundancy: 4.6 % / CC1/2: 0.999 / Net I/σ(I): 13.87
Reflection shellResolution: 2.3→2.38 Å / Num. unique obs: 3435 / CC1/2: 0.862

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→42.37 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.81 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2537 1700 5 %
Rwork0.2058 --
obs0.2082 33996 98.18 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.3→42.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4918 0 32 82 5032
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085100
X-RAY DIFFRACTIONf_angle_d0.9486879
X-RAY DIFFRACTIONf_dihedral_angle_d6.78676
X-RAY DIFFRACTIONf_chiral_restr0.055721
X-RAY DIFFRACTIONf_plane_restr0.012897
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.360.40221360.31832580X-RAY DIFFRACTION95
2.36-2.440.34611440.29472721X-RAY DIFFRACTION100
2.44-2.530.3311420.27912700X-RAY DIFFRACTION99
2.53-2.630.35991410.28342699X-RAY DIFFRACTION99
2.63-2.750.34721430.26462701X-RAY DIFFRACTION100
2.75-2.890.28271420.25022712X-RAY DIFFRACTION99
2.89-3.070.31921440.24182717X-RAY DIFFRACTION99
3.07-3.310.30181410.25082712X-RAY DIFFRACTION99
3.31-3.640.28411420.21582686X-RAY DIFFRACTION98
3.64-4.170.23991370.18682603X-RAY DIFFRACTION95
4.17-5.250.1711430.14992714X-RAY DIFFRACTION98
5.25-100.20241450.16432751X-RAY DIFFRACTION97
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.3745-0.3684-1.54723.06970.18192.3159-0.1730.0847-0.00350.66080.1023-0.03060.08760.02540.09630.569-0.004-0.16040.34070.02070.2951-2.89052.19548.3561
21.984-0.69521.31612.922-0.47013.61940.08370.1706-0.0099-0.35190.0124-0.2355-0.02780.0044-0.1120.3725-0.0075-0.05840.31890.02060.38734.3412-2.464629.1051
36.216-0.35881.0893.5746-0.98553.3704-0.5223-0.13590.7378-0.69780.31960.667-0.8147-0.53250.19850.74210.0143-0.25580.4476-0.0130.5965-2.71564.913522.2064
43.40380.50931.66813.3974-0.23631.97390.0869-0.0762-0.02550.0185-0.1968-0.39880.04730.06560.07850.38850.0284-0.01360.37440.00440.339344.387715.93674.9357
51.81460.2332-1.21732.6111-0.36672.50480.0815-0.11320.0756-0.00960.00010.60940.15330.0193-0.06720.45120.0005-0.07810.3551-0.03720.486724.251311.509676.8746
60.7901-1.35640.24442.3159-0.28435.41080.06160.06410.49440.43440.02490.4968-0.6420.5487-0.32980.5434-0.11010.13520.5249-0.06570.642120.593419.294585.8555
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 132 )
2X-RAY DIFFRACTION2chain 'A' and (resid 133 through 256 )
3X-RAY DIFFRACTION3chain 'A' and (resid 257 through 298 )
4X-RAY DIFFRACTION4chain 'B' and (resid 2 through 132 )
5X-RAY DIFFRACTION5chain 'B' and (resid 133 through 256 )
6X-RAY DIFFRACTION6chain 'B' and (resid 257 through 298 )

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