PDB-5c4l: Conformational alternate of sisomicin in complex with APH(2")-IVa

ID or keywords:

Entry

Database: PDB / ID: 5c4l

Title

Conformational alternate of sisomicin in complex with APH(2")-IVa

Components

APH(2'')-Id

Keywords

TRANSFERASE / Aminoglycoside phosphotransferase / antibiotic resistance

Function / homology

Function and homology information

nucleotide binding / metal ion binding
Similarity search - Function

Biological species

Enterococcus casseliflavus (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.35 Å

Authors

Kaplan, E. / Guichou, J.F. / Berrou, K. / Chaloin, L. / Leban, N. / Lallemand, P. / Barman, T. / Serpersu, E.H. / Lionne, C.

Funding support

France, 1items

Citation

Journal: Biochim.Biophys.Acta / Year: 2016
Title: Aminoglycoside binding and catalysis specificity of aminoglycoside 2-phosphotransferase IVa: A thermodynamic, structural and kinetic study.
Authors: Kaplan, E. / Guichou, J.F. / Chaloin, L. / Kunzelmann, S. / Leban, N. / Serpersu, E.H. / Lionne, C.

History

Deposition	Jun 18, 2015	Deposition site: RCSB / Processing site: PDBE
Revision 1.0	Feb 3, 2016	Provider: repository / Type: Initial release
Revision 1.1	Feb 17, 2016	Group: Database references
Revision 1.2	Jan 10, 2024	Group: Author supporting evidence / Data collection ...Author supporting evidence / Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_audit_support / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5c4l.cif.gz	259.3 KB	Display	PDBx/mmCIF format
PDB format	pdb5c4l.ent.gz	210.6 KB	Display	PDB format
PDBx/mmJSON format	5c4l.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	5c4l_validation.pdf.gz	768.9 KB	Display	wwPDB validaton report
Full document	5c4l_full_validation.pdf.gz	774.8 KB	Display
Data in XML	5c4l_validation.xml.gz	23.1 KB	Display
Data in CIF	5c4l_validation.cif.gz	31.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/c4/5c4l ftp://data.pdbj.org/pub/pdb/validation_reports/c4/5c4l	HTTPS FTP

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Related structure data

Related structure data	5c4kC 4n57S S: Starting model for refinement C: citing same article (ref.)
Similar structure data	5c4k-1 3n4t-d 6cd7-1 4dta-2 4dt8-2 4de4-2 4de4-1 5c4k-2 4dt9-1 4dfb-1 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) 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

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

1

A: APH(2'')-Id

hetero molecules

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

Unit cell

Length a, b, c (Å)	74.220, 65.040, 78.780
Angle α, β, γ (deg.)	90.000, 91.180, 90.000
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	APH(2'')-Id Mass: 37595.852 Da / Num. of mol.: 2 / Mutation: E26Q, E30K 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-4XR / (2S,3R)-3-amino-6-(aminomethyl)-3,4-dihydro-2H-pyran-2-ol Mass: 144.172 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C₆H₁₂N₂O₂
#3: Chemical	ChemComp-SIS / (1S,2S,3R,4S,6R)-4,6-diamino-3-{[(2S,3R)-3-amino-6-(aminomethyl)-3,4-dihydro-2H-pyran-2-yl]oxy}-2-hydroxycyclohexyl 3-deoxy-4-C-methyl-3-(methylamino)-beta-L-arabinopyranoside / Sisomicin Mass: 447.526 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₉H₃₇N₅O₇ / Comment: antibiotic*YM
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 55 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.72 Å³/Da / Density % sol: 54.79 %
Crystal grow	Temperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 7.6 / Details: 12% PEG3350, 50-90 mM Ammonium citrate / PH range: 7.0 - 7.9

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.972957 Å
Detector	Type: PSI PILATUS 6M / Detector: PIXEL / Date: Mar 14, 2015
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.972957 Å / Relative weight: 1
Reflection	Resolution: 2.35→37.1 Å / Num. all: 29965 / Num. obs: 28377 / % possible obs: 94.7 % / Redundancy: 1.9 % / R_merge(I) obs: 0.034 / Net I/σ(I): 8.9
Reflection shell	Resolution: 2.35→2.43 Å / Redundancy: 1.9 % / R_merge(I) obs: 0.23 / Mean I/σ(I) obs: 2.5 / % possible all: 96.6

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0073	refinement
SCALA		data scaling
PDB_EXTRACT	3.15	data extraction
Coot		model building
DNA		data collection

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 4N57

4n57

Resolution: 2.35→37.1 Å / Cor.coef. F_o:F_c: 0.95 / Cor.coef. F_o:F_c free: 0.927 / SU B: 25.533 / SU ML: 0.276 / Cross valid method: THROUGHOUT / ESU R: 0.425 / ESU R Free: 0.284 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2784	1392	4.7 %	RANDOM
R_work	0.227	-	-	-
obs	0.2296	28377	94.7 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK

Displacement parameters

B_iso max: 130.8 Å² / B_iso mean: 63.306 Å² / B_iso min: 23.6 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	8.43 Å²	-0 Å²	-1.09 Å²
2-	-	-6.4 Å²	-0 Å²
3-	-	-	-1.98 Å²

Refinement step

Cycle: final / Resolution: 2.35→37.1 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4876	0	41	55	4972
B_iso mean	-	-	71.98	47.4	-
Num. residues	-	-	-	-	594

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.013	0.02	5056
X-RAY DIFFRACTION	r_bond_other_d	0.005	0.02	4748
X-RAY DIFFRACTION	r_angle_refined_deg	1.538	1.969	6829
X-RAY DIFFRACTION	r_angle_other_deg	1.225	3.006	10971
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.86	5	596
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	35.211	24.844	256
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	18.778	15	910
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	20.228	15	21
X-RAY DIFFRACTION	r_chiral_restr	0.091	0.2	730
X-RAY DIFFRACTION	r_gen_planes_refined	0.008	0.021	5658
X-RAY DIFFRACTION	r_gen_planes_other	0.004	0.02	1175
X-RAY DIFFRACTION	r_mcbond_it	2.726	3.633	2381
X-RAY DIFFRACTION	r_mcbond_other	2.726	3.632	2380
X-RAY DIFFRACTION	r_mcangle_it	4.13	5.444	2975

LS refinement shell

Resolution: 2.35→2.411 Å

	R_factor	Num. reflection	% reflection
R_free	0.417	104	-
R_work	-	2133	-
obs	-	-	96.46 %

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	1.7173	-0.4502	0.4803	2.9405	-0.0143	2.1143	-0.0159	-0.1418	0.0766	0.0728	0.0083	-0.1939	0.0238	0.1805	0.0075	0.2316	-0.0114	-0.008	0.2117	-0.0024	0.2054	52.9533	5.3161	84.7179
2	4.5881	0.0814	-2.7931	7.4983	-3.0663	12.0141	-0.0481	0.3426	0.2871	-0.164	0.1468	0.0416	-0.0589	-0.1195	-0.0987	0.1743	0.0261	-0.0892	0.1685	-0.0534	0.2005	46.1276	1.2161	83.2188
3	3.6802	-0.4337	2.7202	2.1312	-1.0008	4.9141	0.0443	0.1894	-0.1126	-0.0967	0.0086	-0.0776	0.1821	0.1965	-0.053	0.2025	0.0018	0.0217	0.1721	-0.0123	0.2406	45.4773	-7.6487	75.472
4	3.1364	-1.8028	1.9179	2.867	-2.0302	3.6139	0.1331	0.4126	0.1731	-0.3792	-0.0596	0.2238	-0.0066	-0.0844	-0.0734	0.2644	-0.0476	0.028	0.2294	-0.0534	0.3005	39.3701	5.6999	70.4948
5	2.5021	-1.8301	1.2896	8.0961	-4.6353	5.3372	0.0483	0.151	0.0681	-0.3443	-0.1515	-0.1092	0.1165	0.1257	0.1032	0.166	-0.0272	0.0065	0.2462	-0.0497	0.2465	33.3506	-8.463	66.5781
6	0.7618	-0.8863	-2.2992	2.8464	4.4418	8.8811	-0.0693	-0.1036	-0.1592	0.2207	0.0794	-0.1001	0.4175	0.2363	-0.0101	0.2777	0.0023	-0.013	0.2887	0.0155	0.3083	20.9739	-8.0932	90.6463
7	1.936	-1.8199	-3.1234	4.8957	4.6832	6.1777	0.0144	-0.0099	-0.0366	0.382	-0.1647	0.1557	0.3125	-0.2779	0.1503	0.3253	-0.005	-0.0118	0.3243	0.0375	0.3345	11.6693	-4.3905	89.628
8	1.6835	0.1031	0.8233	2.5446	-0.4084	1.7091	-0.0374	0.1816	0.3613	-0.1526	0.0588	0.2184	-0.2741	-0.1423	-0.0214	0.1763	0.0198	0.0189	0.1857	-0.0105	0.1712	27.6856	-0.7066	67.8982
9	9.7543	3.1457	4.7697	7.0627	3.247	9.2576	-0.0113	0.5471	-0.0712	-0.2855	0.0351	0.0293	0.0567	0.3744	-0.0239	0.2384	0.0184	0.0478	0.218	0.0098	0.2684	21.0297	1.8236	85.7023
10	13.253	-2.2132	-3.2801	2.1669	1.0985	2.8824	-0.0571	-0.4159	0.1057	0.2827	0.0951	-0.1293	0.0277	0.2035	-0.0381	0.3504	-0.0156	-0.0075	0.2791	0.0082	0.2997	22.6888	8.1806	92.2319
11	6.5615	-0.8641	0.648	8.5085	-1.5849	0.6287	-0.0443	-0.057	-0.0131	0.1332	0.1303	0.3415	-0.0904	-0.3812	-0.086	0.2307	0.0309	0.0113	0.4291	-0.0001	0.2959	-18.4289	-9.0084	131.0001
12	2.0413	0.1479	0.3179	2.5223	0.0304	3.6395	-0.001	-0.0295	-0.1323	0.0275	0.0086	0.0137	0.1322	-0.0246	-0.0077	0.2169	0.0171	0.0054	0.2369	-0.0039	0.2734	-9.8634	-9.62	132.0639
13	19.6646	-3.6962	5.2221	9.21	-1.3884	5.6188	0.2326	0.2319	-0.2253	-0.1415	-0.1402	0.0179	0.3423	0.253	-0.0925	0.2687	-0.0235	0.0728	0.2125	-0.0216	0.1934	-4.9699	-22.2888	123.7954
14	3.9194	0.8894	-0.5032	1.8975	0.3074	2.7217	0.0495	-0.2304	-0.4013	-0.01	-0.0343	0.0973	0.2227	-0.1041	-0.0153	0.3332	0.0143	0.0028	0.2278	0.0174	0.2712	-5.0493	-19.0258	129.3547
15	1.454	0.126	-0.1081	4.7821	0.1426	1.83	0.0047	-0.0799	0.1426	0.0405	-0.025	-0.3996	-0.1895	0.2548	0.0204	0.2548	0.0323	-0.0094	0.3193	0.0061	0.2073	12.7004	-14.1451	120.3351
16	4.7639	-4.9499	6.7482	6.0414	-6.8282	10.1065	-0.0093	-0.5505	-0.402	0.1895	0.2567	0.4638	0.0837	-0.7691	-0.2474	0.2307	-0.0147	0.0193	0.2612	0.0121	0.2791	-5.3924	-25.5848	102.449
17	2.5999	-0.8291	1.5028	0.8791	-0.6196	2.2892	0.0372	0.1739	0.0795	-0.1819	-0.068	0.1289	-0.1514	-0.0244	0.0307	0.2579	-0.0409	0.0298	0.221	0.0092	0.2794	-2.1929	-18.7867	99.1957
18	1.5796	0.3947	-0.1057	2.6014	1.1171	2.4753	0.0079	-0.1222	0.3434	0.0279	0.0899	-0.2939	-0.3501	0.3544	-0.0978	0.2087	0.0164	-0.0117	0.2209	0.0288	0.2327	12.1543	-13.4359	113.821
19	12.3046	-0.2164	2.6855	2.7554	0.3361	0.6561	-0.0174	-0.2213	-0.073	0.1023	-0.0063	0.0575	0.0265	-0.0024	0.0237	0.2585	-0.0013	-0.0018	0.2011	0.0123	0.206	-1.9832	-12.7978	101.8245
20	8.3892	1.8383	-3.0018	6.8791	0.1304	10.4711	0.1089	-0.3159	0.0582	0.3391	-0.0544	0.2017	-0.2749	-0.1725	-0.0546	0.2849	0.0305	-0.039	0.2772	-0.0085	0.3489	-10.9392	-6.7752	101.7178

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	1 - 40
2	X-RAY DIFFRACTION	2	A	41 - 55
3	X-RAY DIFFRACTION	3	A	56 - 86
4	X-RAY DIFFRACTION	4	A	87 - 115
5	X-RAY DIFFRACTION	5	A	116 - 143
6	X-RAY DIFFRACTION	6	A	144 - 161
7	X-RAY DIFFRACTION	7	A	162 - 187
8	X-RAY DIFFRACTION	8	A	188 - 264
9	X-RAY DIFFRACTION	9	A	265 - 280
10	X-RAY DIFFRACTION	10	A	281 - 297
11	X-RAY DIFFRACTION	11	B	1 - 14
12	X-RAY DIFFRACTION	12	B	15 - 50
13	X-RAY DIFFRACTION	13	B	51 - 68
14	X-RAY DIFFRACTION	14	B	69 - 97
15	X-RAY DIFFRACTION	15	B	98 - 142
16	X-RAY DIFFRACTION	16	B	143 - 155
17	X-RAY DIFFRACTION	17	B	156 - 202
18	X-RAY DIFFRACTION	18	B	203 - 263
19	X-RAY DIFFRACTION	19	B	264 - 279
20	X-RAY DIFFRACTION	20	B	280 - 297

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