PDB-4ork: Crystal Structure of the Phosphotransferase Domain of the Bifunct...

ID or keywords:

Entry

Database: PDB / ID: 4ork

Title

Crystal Structure of the Phosphotransferase Domain of the Bifunctional Aminoglycoside Resistance Enzyme AAC(6')-Ie-APH(2'')-Ia

Components

Bifunctional AAC/APH

Keywords

TRANSFERASE /

kinase /

antibiotic resistance / aminoglycosides and GTP

Function / homology

Function and homology information

aminoglycoside phosphotransferase activity / aminoglycoside 2''-phosphotransferase /

N-acyltransferase activity /

Transferases; Acyltransferases; Transferring groups other than aminoacyl groups /

phosphorylation / response to antibiotic /

ATP binding /

cytoplasm
Similarity search - Function

Biological species

Staphylococcus aureus (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON / Resolution: 2.3 Å

Authors

Smith, C.A. / Toth, M. / Bhattacharya, M. / Frase, H. / Vakulenko, S.B.

Citation

Journal: Acta Crystallogr.,Sect.D / Year: 2014
Title: Structure of the phosphotransferase domain of the bifunctional aminoglycoside-resistance enzyme AAC(6')-Ie-APH(2'')-Ia.
Authors: Smith, C.A. / Toth, M. / Bhattacharya, M. / Frase, H. / Vakulenko, S.B.

History

Deposition	Feb 11, 2014	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jul 2, 2014	Provider: repository / Type: Initial release
Revision 1.1	Feb 28, 2024	Group: Data collection / Database references / Derived calculations Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4ork.cif.gz	503.8 KB	Display	PDBx/mmCIF format
PDB format	pdb4ork.ent.gz	419.9 KB	Display	PDB format
PDBx/mmJSON format	4ork.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/or/4ork ftp://data.pdbj.org/pub/pdb/validation_reports/or/4ork	HTTPS FTP

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Related structure data

Similar structure data	5iqf-4 5iqb-1 6cav-4 5iqb-2 6cgd-1 3tih-2 5iqe-4 6cav-2 6cgg-2 5iqi-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) 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

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#146 - Feb 2012 Aminoglycoside Antibiotics similarity (5) #97 - Jan 2008 Circadian Clock Proteins similarity (3)

Deposited unit

A: Bifunctional AAC/APH

B: Bifunctional AAC/APH

C: Bifunctional AAC/APH

D: Bifunctional AAC/APH

hetero molecules

146 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Bifunctional AAC/APH

hetero molecules

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

2

B: Bifunctional AAC/APH

hetero molecules

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

3

C: Bifunctional AAC/APH

hetero molecules

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

4

D: Bifunctional AAC/APH

hetero molecules

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

Unit cell

Length a, b, c (Å)	90.685, 95.697, 91.149
Angle α, β, γ (deg.)	90.00, 104.88, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Bifunctional AAC/APH / 6'-aminoglycoside N-acetyltransferase / AAC(6') / 2''-aminoglycoside phosphotransferase / APH(2'') Mass: 35948.199 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: aacA-aphD, R015, VRA0030 / Production host: Escherichia coli (E. coli) References: UniProt: P0A0C1, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups, Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor
#2: Chemical	ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE / Guanosine diphosphate Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₁₀H₁₅N₅O₁₁P₂ / Comment: GDP, energy-carrying molecule*YM
#3: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 207 / 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: 2.66 Å³/Da / Density % sol: 53.73 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.2 M MgCl2, 0.1 M Hepes, pH 7.5, 30% PEG400, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 21, 2012
Radiation	Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9795 Å / Relative weight: 1
Reflection	Resolution: 2.3→36.2 Å / Num. all: 62509 / Num. obs: 62509 / % possible obs: 93.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.5 % / B_iso Wilson estimate: 60.5 Å² / R_merge(I) obs: 0.038 / Net I/σ(I): 13.6
Reflection shell	Resolution: 2.3→2.35 Å / R_merge(I) obs: 0.51 / Mean I/σ(I) obs: 1.6 / % possible all: 96.6

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Processing

Software

Name	Version	Classification
Blu-Ice		data collection
SOLVE		phasing
PHENIX	(phenix.refine: 1.8.4_1496)	refinement
XDS		data reduction
SCALA		data scaling

Refinement

Resolution: 2.3→36.2 Å / SU ML: 0.32 / σ(F): 1.36 / Phase error: 29.86 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2449	3118	4.99 %	random
R_work	0.1852	-	-	-
obs	0.1882	62509	93.31 %	-

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 2.3→36.2 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	9752	0	120	207	10079

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.009	10120
X-RAY DIFFRACTION	f_angle_d	1.204	13611
X-RAY DIFFRACTION	f_dihedral_angle_d	16.332	3785
X-RAY DIFFRACTION	f_chiral_restr	0.049	1482
X-RAY DIFFRACTION	f_plane_restr	0.005	1736

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 (%)
2.3-2.336	0.3571	133	0.2859	2813	X-RAY DIFFRACTION	96
2.336-2.3743	0.3454	130	0.2897	2774	X-RAY DIFFRACTION	96
2.3743-2.4152	0.3279	157	0.2754	2749	X-RAY DIFFRACTION	96
2.4152-2.4591	0.3104	137	0.2716	2765	X-RAY DIFFRACTION	95
2.4591-2.5064	0.3201	150	0.2585	2710	X-RAY DIFFRACTION	95
2.5064-2.5575	0.3213	135	0.2575	2613	X-RAY DIFFRACTION	91
2.5575-2.6131	0.3442	136	0.2476	2762	X-RAY DIFFRACTION	95
2.6131-2.6739	0.311	140	0.2387	2798	X-RAY DIFFRACTION	96
2.6739-2.7407	0.3037	155	0.2382	2748	X-RAY DIFFRACTION	96
2.7407-2.8148	0.3649	153	0.243	2759	X-RAY DIFFRACTION	96
2.8148-2.8976	0.3154	146	0.2301	2706	X-RAY DIFFRACTION	94
2.8976-2.9911	0.2942	144	0.2253	2703	X-RAY DIFFRACTION	93
2.9911-3.0979	0.2806	149	0.2266	2615	X-RAY DIFFRACTION	92
3.0979-3.2219	0.275	123	0.2112	2639	X-RAY DIFFRACTION	91
3.2219-3.3684	0.3044	125	0.2139	2749	X-RAY DIFFRACTION	94
3.3684-3.5459	0.267	161	0.1987	2644	X-RAY DIFFRACTION	93
3.5459-3.7678	0.2422	140	0.1762	2611	X-RAY DIFFRACTION	90
3.7678-4.0584	0.2031	131	0.1562	2528	X-RAY DIFFRACTION	88
4.0584-4.4662	0.1981	151	0.1395	2605	X-RAY DIFFRACTION	90
4.4662-5.1109	0.1866	143	0.1402	2710	X-RAY DIFFRACTION	93
5.1109-6.4333	0.2426	145	0.1643	2628	X-RAY DIFFRACTION	90
6.4333-36.2228	0.1898	134	0.1549	2762	X-RAY DIFFRACTION	92

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	2.4248	-0.2066	-0.7759	0.8795	-0.1037	4.6457	0.034	-0.1668	0.046	0.0308	-0.0837	-0.073	-0.2346	-0.0395	0.0086	0.438	-0.0036	-0.0104	0.5488	0.0822	0.4894	69.688	21.0512	44.3828
2	1.6564	-0.8643	-0.5106	3.1642	-0.4553	1.8735	0.1071	-0.0125	-0.3906	-0.2339	-0.093	-0.3587	0.0403	0.2427	0.07	0.4209	-0.0287	0.0329	0.5162	-0.0194	0.3558	79.4493	27.3065	24.8932
3	3.2486	-1.4344	0.1932	2.0636	-0.6162	1.3182	0.0002	0.2145	0.4021	0.066	0.1034	0.0704	-0.1838	-0.2208	-0.0193	0.4901	-0.0153	-0.002	0.5637	0.1459	0.5311	59.2315	48.851	30.5865
4	3.6479	-0.4672	0.8689	2.5938	-0.7016	2.6376	0.0448	-0.0391	0.2379	-0.0862	-0.0924	-0.3496	-0.191	0.2575	0.0072	0.4214	-0.0407	0.0354	0.5556	0.0194	0.4296	78.0385	32.3163	27.0739
5	1.6283	0.6072	0.7737	2.828	0.3316	0.3257	-0.0206	-0.3263	0.4138	0.4133	0.1184	-0.3307	0.3236	0.0177	-0.0065	0.5807	0.0711	-0.0185	0.6002	0.0292	0.5796	69.0962	47.6423	34.2855
6	1.5769	0.3511	0.9453	0.9063	1.6384	5.5882	-0.0854	-0.1568	0.0044	-0.1694	-0.18	0.0654	-0.3991	0.0184	0.2079	0.6508	0.0427	-0.0453	0.4304	0.0398	0.5056	42.9283	10.8355	24.0887
7	0.9954	-0.2489	0.2842	2.8026	1.127	1.7619	-0.0746	0.0747	0.298	-0.2904	-0.1388	0.2058	-0.2976	-0.1984	0.1413	0.523	0.0939	-0.069	0.47	0.1143	0.4842	33.6722	4.9436	4.2915
8	2.4785	-0.9498	0.7429	1.7747	-0.5338	1.5612	-0.1806	0.1681	-0.2539	0.0583	-0.0068	-0.1486	0.0094	0.1024	0.2449	0.4449	-0.0473	0.0408	0.3223	0.0229	0.466	53.372	-16.818	8.9396
9	3.5575	-0.8397	1.0572	1.9769	0.3045	3.2446	-0.0803	-0.1965	-0.134	-0.0985	-0.0485	0.0453	-0.0261	-0.3256	0.1409	0.5169	0.0261	-0.0754	0.3836	0.0651	0.4963	35.1238	-0.1074	6.0475
10	1.4583	-0.4321	-0.5976	2.4615	-0.369	0.7295	-0.1457	-0.0343	-0.0512	0.3542	0.0147	0.3722	-0.2198	-0.1475	0.1895	0.5316	0.0174	-0.0387	0.2794	0.0596	0.5334	43.5868	-15.2378	12.9234
11	1.7669	0.1715	0.0553	1.9331	-1.369	3.8914	0.1644	0.2796	0.082	-0.3729	-0.2773	-0.0384	0.3258	0.5467	0.1385	0.4788	0.0498	0.0058	0.6129	0.0696	0.4764	54.5797	3.8225	49.0933
12	4.6501	-1.134	0.2621	2.5108	-0.9133	3.784	-0.0202	-0.1868	-0.4725	0.2998	0.0683	-0.2473	0.2166	0.4169	-0.0485	0.3333	0.0251	0.0247	0.52	0.1119	0.4329	49.188	-6.6331	69.0273
13	3.1112	-1.4213	0.4217	1.5411	0.5781	0.7668	-0.3169	-0.0707	0.1309	0.1921	0.1565	0.0655	-0.289	-0.0086	0.1253	0.581	-0.0506	0.1382	0.395	-0.0552	0.5904	26.9246	13.164	67.3212
14	1.8229	-1.1555	-0.4214	2.1495	-0.3805	2.6225	-0.0362	-0.1538	-0.3292	0.0592	0.0645	0.4284	0.0633	-0.1233	-0.0119	0.4465	-0.0324	0.0121	0.5033	-0.008	0.5066	44.1587	-5.2421	67.4349
15	3.2679	-1.2568	0.866	1.532	-0.0821	2.0957	0.0046	0.1615	-0.3659	-0.0627	-0.0159	0.2394	0.1569	0.1744	0.0637	0.4768	-0.0268	0.1297	0.404	-0.054	0.5806	28.0132	3.7838	62.6113
16	2.0918	0.324	-0.3272	2.5557	1.7088	1.8625	0.2426	0.5398	0.1042	-0.3742	-0.4064	0.1577	-0.2619	-1.2038	0.0839	0.4292	0.1284	-0.0265	1.0186	0.0636	0.4726	58.5217	27.7224	69.4111
17	2.0321	-0.407	1.2664	0.7582	0.4245	1.7937	0.0355	0.4309	0.2401	-0.2562	-0.221	0.1493	-0.4576	-0.8483	0.1411	0.7733	0.1621	0.1419	0.8059	0.0329	0.5671	63.4512	37.4916	89.2355
18	2.99	-0.2864	-0.0417	1.7672	-0.3661	1.8468	-0.4025	-0.0898	-0.8599	0.0787	0.1032	-0.0426	0.6476	-0.1571	0.2351	0.5136	-0.0636	0.0596	0.318	-0.0512	0.5145	85.9671	17.6645	88.4257
19	2.1259	-1.89	-0.5721	2.4695	-0.6627	2.6452	0.2291	0.5738	0.4918	0.1566	-0.0674	-0.0901	-0.521	-0.3221	-0.1313	0.5289	0.0089	0.0356	0.5893	0.0399	0.5975	68.5294	36.0562	88.0483
20	2.7199	-0.2884	-1.5088	1.2952	0.4563	1.5368	-0.1371	0.201	-0.0587	-0.0297	0.0026	0.0684	0.0343	-0.302	0.1137	0.4578	-0.005	-0.0035	0.4754	-0.0528	0.4978	85.0256	27.213	83.9913

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain A and resid 6 through 105
2	X-RAY DIFFRACTION	2	chain A and resid 106 through 148
3	X-RAY DIFFRACTION	3	chain A and resid 149 through 194
4	X-RAY DIFFRACTION	4	chain A and resid 195 through 256
5	X-RAY DIFFRACTION	5	chain A and resid 257 through 304
6	X-RAY DIFFRACTION	6	chain B and resid 6 through 105
7	X-RAY DIFFRACTION	7	chain B and resid 106 through 148
8	X-RAY DIFFRACTION	8	chain B and resid 149 through 194
9	X-RAY DIFFRACTION	9	chain B and resid 195 through 256
10	X-RAY DIFFRACTION	10	chain B and resid 257 through 304
11	X-RAY DIFFRACTION	11	chain C and resid 9 through 105
12	X-RAY DIFFRACTION	12	chain C and resid 106 through 148
13	X-RAY DIFFRACTION	13	chain C and resid 149 through 194
14	X-RAY DIFFRACTION	14	chain C and resid 195 through 256
15	X-RAY DIFFRACTION	15	chain C and resid 257 through 304
16	X-RAY DIFFRACTION	16	chain D and resid 9 through 105
17	X-RAY DIFFRACTION	17	chain D and resid 106 through 148
18	X-RAY DIFFRACTION	18	chain D and resid 149 through 194
19	X-RAY DIFFRACTION	19	chain D and resid 195 through 256
20	X-RAY DIFFRACTION	20	chain D and resid 257 through 305

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