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

ID or keywords:

Entry

Database: PDB / ID: 9qmr

Title

APH(2'')-Id with a fragment

Components

APH(2'')-Id

Keywords

ANTIBIOTIC / 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 species

Enterococcus casseliflavus (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.78 Å

Authors

Guichou, J.F. / Gelin, M. / Tomaszczyk, M. / Kowalewski, J. / Lionne, C.

Funding support

France, 3items

Organization	Grant number	Country
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

Citation

Journal: 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

Deposition	Mar 24, 2025	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Feb 11, 2026	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9qmr.cif.gz	266 KB	Display	PDBx/mmCIF format
PDB format	pdb9qmr.ent.gz		Display	PDB format
PDBx/mmJSON format	9qmr.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/qm/9qmr ftp://data.pdbj.org/pub/pdb/validation_reports/qm/9qmr	HTTPS FTP

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Related structure data

Related structure data	9qn6C 9qnnC 9qnqC 9qnsC 9qnwC 9qnxC 9qnyC 9qodC 9qoeC 9qokC 9qolC 9qomC 9qosC 9qp9C 9qpbC 9qpdC 9qplC C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#146 - Feb 2012 Aminoglycoside Antibiotics similarity (2)

Deposited unit

A: APH(2'')-Id

B: APH(2'')-Id

hetero molecules

76.4 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: APH(2'')-Id

hetero molecules

defined by author
Evidence: gel filtration
38 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: APH(2'')-Id

hetero molecules

defined by author
38.4 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	75.286, 65.430, 77.475
Angle α, β, γ (deg.)	90.00, 91.35, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#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-A1I7K / 7-bromanyl-3,4-dihydro-2~{H}-pyrido[3,2-b][1,4]oxazine Mass: 215.047 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₇H₇BrN₂O / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-DMS / DIMETHYL SULFOXIDE Mass: 78.133 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C₂H₆OS / Comment: DMSO, precipitant*YM
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 193 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y
Has protein modification	N

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.54 Å³/Da / Density % sol: 51.52 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, hanging drop / Details: 12% PEG3350, 50-90 mM Ammonium citrate

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.9798 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 9, 2018
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9798 Å / Relative weight: 1
Reflection	Resolution: 1.78→41.35 Å / Num. obs: 71454 / % possible obs: 98.84 % / Redundancy: 3 % / CC_1/2: 0.999 / Net I/σ(I): 15.88
Reflection shell	Resolution: 1.78→1.84 Å / R_merge(I) obs: 1.8 / Num. unique obs: 7176 / CC_1/2: 0.738

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Processing

Software

Name	Version	Classification
PHENIX	(1.20.1_4487: ???)	refinement
XDS		data reduction
XDS		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.78→41.35 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.41 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2296	3528	4.94 %
R_work	0.1979	-	-
obs	0.1994	71438	98.84 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 1.78→41.35 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4892	0	62	193	5147

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	5124
X-RAY DIFFRACTION	f_angle_d	0.968	6910
X-RAY DIFFRACTION	f_dihedral_angle_d	5.394	683
X-RAY DIFFRACTION	f_chiral_restr	0.06	724
X-RAY DIFFRACTION	f_plane_restr	0.008	908

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
1.78-1.8	0.3809	134	0.3358	2699	X-RAY DIFFRACTION	100
1.8-1.83	0.3419	140	0.3026	2724	X-RAY DIFFRACTION	100
1.83-1.86	0.3137	148	0.2764	2732	X-RAY DIFFRACTION	100
1.86-1.89	0.2815	127	0.2599	2736	X-RAY DIFFRACTION	100
1.89-1.92	0.3247	104	0.2643	2753	X-RAY DIFFRACTION	99
1.92-1.95	0.2773	137	0.2478	2694	X-RAY DIFFRACTION	99
1.95-1.99	0.2812	151	0.2471	2759	X-RAY DIFFRACTION	100
1.99-2.02	0.2956	148	0.2552	2659	X-RAY DIFFRACTION	99
2.02-2.07	0.3153	154	0.2531	2705	X-RAY DIFFRACTION	100
2.07-2.11	0.2716	197	0.2262	2702	X-RAY DIFFRACTION	100
2.11-2.16	0.2895	149	0.2179	2714	X-RAY DIFFRACTION	100
2.16-2.21	0.2561	167	0.2159	2708	X-RAY DIFFRACTION	100
2.21-2.27	0.2473	122	0.2162	2722	X-RAY DIFFRACTION	99
2.27-2.34	0.2783	130	0.2134	2688	X-RAY DIFFRACTION	98
2.34-2.42	0.2676	139	0.2205	2729	X-RAY DIFFRACTION	99
2.42-2.5	0.2456	140	0.228	2724	X-RAY DIFFRACTION	99
2.5-2.6	0.2643	132	0.2315	2739	X-RAY DIFFRACTION	99
2.6-2.72	0.2642	126	0.2309	2704	X-RAY DIFFRACTION	99
2.72-2.86	0.2676	157	0.2358	2700	X-RAY DIFFRACTION	99
2.86-3.04	0.2296	154	0.2137	2675	X-RAY DIFFRACTION	97
3.04-3.28	0.2598	152	0.2139	2690	X-RAY DIFFRACTION	98
3.28-3.61	0.1957	135	0.1908	2697	X-RAY DIFFRACTION	98
3.61-4.13	0.2232	114	0.1786	2743	X-RAY DIFFRACTION	98
4.13-5.2	0.1718	122	0.1434	2746	X-RAY DIFFRACTION	98
5.2-41.35	0.1793	149	0.1657	2768	X-RAY DIFFRACTION	97

Refinement TLS params.

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

ID	L11 (°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)
1	2.1125	-0.6171	-0.7394	2.678	0.2527	2.1057	-0.1736	-0.0245	-0.0372	0.5482	0.0963	0.139	0.0821	-0.0194	0.0706	0.3589	-0.0049	-0.0178	0.2807	0.008	0.2423	-2.293	2.4135	48.0768
2	1.2492	-0.7531	0.7505	1.5479	-1.0507	2.4342	0.0831	0.1604	-0.1033	-0.3878	0.0302	0.0469	0.0699	-0.1111	-0.1151	0.3213	-0.005	-0.0156	0.347	0.0107	0.3343	2.5858	-2.8673	28.2765
3	3.1005	0.3562	1.1673	2.1501	0.1921	3.1048	-0.2657	0.0041	0.4004	-0.4671	0.1373	-0.0055	-0.3831	-0.0513	0.1081	0.4073	-0.0242	-0.0085	0.3541	0.0045	0.3792	4.1062	3.6328	24.6345
4	2.8099	0.2721	1.2276	1.8931	0.2797	1.9156	0.1156	0.0592	-0.0102	0.023	-0.0974	-0.2769	0.0979	0.1455	-0.0212	0.2485	0.0245	0.0438	0.2952	0.0312	0.2916	45.087	15.9609	74.6306
5	2.2998	0.223	-0.9453	2.6774	0.3798	1.9782	0.0608	-0.1693	0.1216	0.4226	-0.0693	0.5109	0.0957	-0.0062	0.0257	0.3015	0.015	0.0425	0.2273	-0.0399	0.2788	23.8978	13.3497	78.5243

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 1 through 132 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 133 through 240 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 241 through 297 )
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 1 through 132 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 133 through 297 )

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