PDB-5luh: AadA E87Q in complex with ATP, calcium and streptomycin

ID or keywords:

Entry

Database: PDB / ID: 5luh

Title

AadA E87Q in complex with ATP, calcium and streptomycin

Components

Streptomycin 3''-adenylyltransferase

Keywords

TRANSFERASE / AMINOGLYCOSIDE ADENYL TRANSFERASE / ANT(3'')9 / ANTIBIOTIC RESISTANCE

Function / homology

Function and homology information

streptomycin 3''-adenylyltransferase / aminoglycoside 3''-adenylyltransferase activity / adenylyltransferase activity / response to antibiotic / ATP binding / metal ion binding
Similarity search - Function

Biological species

Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.73 Å

Authors

Stern, A.L. / Van der Verren, S.E. / Selmer, M.

Funding support

Sweden, 2items

Citation

Journal: J.Biol.Chem. / Year: 2018
Title: Structural mechanism of AadA, a dual-specificity aminoglycoside adenylyltransferase fromSalmonella enterica.
Authors: Stern, A.L. / Van der Verren, S.E. / Kanchugal P, S. / Nasvall, J. / Gutierrez-de-Teran, H. / Selmer, M.

History

Deposition	Sep 8, 2016	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jan 17, 2018	Provider: repository / Type: Initial release
Revision 1.1	Jun 12, 2019	Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2	Jan 17, 2024	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn 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_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.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.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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_conn.ptnr2_label_seq_id
Revision 1.3	Nov 6, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5luh.cif.gz	248.6 KB	Display	PDBx/mmCIF format
PDB format	pdb5luh.ent.gz	198.3 KB	Display	PDB format
PDBx/mmJSON format	5luh.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	5luh_validation.pdf.gz	2.3 MB	Display	wwPDB validaton report
Full document	5luh_full_validation.pdf.gz	2.3 MB	Display
Data in XML	5luh_validation.xml.gz	27.4 KB	Display
Data in CIF	5luh_validation.cif.gz	40.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/lu/5luh ftp://data.pdbj.org/pub/pdb/validation_reports/lu/5luh	HTTPS FTP

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Related structure data

Related structure data	5g4aSC 5lpaC 6fzbC 4cs6 C: citing same article (ref.) S: Starting model for refinement
Similar structure data	5g4a-1 3cuh-d 5g4a-2 3aay-2 6jdz-1 4pmy-1 1h4k-d 6je2-1 6je1-2 5lpa-2 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	#106 - Oct 2008 Poly(A) Polymerase similarity (2) #10 - Oct 2000 Ribosome similarity (1) #226 - Oct 2018 Aminoglycoside Antibiotics and Resistance similarity (1)

Deposited unit

A: Streptomycin 3''-adenylyltransferase

B: Streptomycin 3''-adenylyltransferase

hetero molecules

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

1

A: Streptomycin 3''-adenylyltransferase

hetero molecules

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

2

B: Streptomycin 3''-adenylyltransferase

hetero molecules

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

Unit cell

Length a, b, c (Å)	82.472, 82.472, 79.174
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	145
Space group name H-M	P3₂

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Protein , 1 types, 2 molecules AB

#1: Protein	Streptomycin 3''-adenylyltransferase Mass: 30527.053 Da / Num. of mol.: 2 / Mutation: E87Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium (bacteria) Gene: aadA, STM1264 / Plasmid: pEXP5-CT / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: Q8ZPX9, streptomycin 3''-adenylyltransferase

#1: Protein

Streptomycin 3''-adenylyltransferase

Mass: 30527.053 Da / Num. of mol.: 2 / Mutation: E87Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Gene: aadA, STM1264 / Plasmid: pEXP5-CT / Production host:

Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q8ZPX9, streptomycin 3''-adenylyltransferase

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Non-polymers , 7 types, 531 molecules

#2: Chemical	ChemComp-CA / CALCIUM ION Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#3: Chemical	ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₀H₁₆N₅O₁₃P₃ / Comment: ATP, energy-carrying molecule*YM
#4: Chemical	ChemComp-SRY / STREPTOMYCIN / STREPTOMYCIN A Mass: 581.574 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂₁H₃₉N₇O₁₂ / Comment: antibiotic*YM
#5: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂H₆O₂
#6: Chemical	ChemComp-PEG / DI(HYDROXYETHYL)ETHER Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₄H₁₀O₃
#7: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#8: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 518 / Source method: isolated from a natural source / Formula: H₂O

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Details

Has protein modification	Y

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 1.92 Å³/Da / Density % sol: 36 %
Crystal grow	Temperature: 281 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 20% (w/v) PEG 6000, 0.2 M CaCl2, 0.1 M Hepes pH 7.5

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.972 Å
Detector	Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 17, 2015
Radiation	Monochromator: liquid nitrogen cooled channel-cut silicon monochromator Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.972 Å / Relative weight: 1
Reflection	Resolution: 1.73→36.58 Å / Num. obs: 122414 / % possible obs: 97 % / Redundancy: 2.63 % / CC_1/2: 0.989 / R_merge(I) obs: 0.171 / Net I/σ(I): 5.22
Reflection shell	Resolution: 1.73→1.83 Å / R_merge(I) obs: 0.928 / Mean I/σ(I) obs: 0.98 / CC_1/2: 0.273 / % possible all: 99.2

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Processing

Software

Name	Version	Classification
PHENIX	(1.10_2155: ???)	refinement
XDS		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 5g4a

5g4a

Resolution: 1.73→36.573 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 0.87 / Phase error: 25.36

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2257	6130	5.07 %	Random selection
R_work	0.1885	-	-	-
obs	0.1904	121007	96.25 %	-

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Displacement parameters

B_iso mean: 29.8 Å²

Refinement step

Cycle: LAST / Resolution: 1.73→36.573 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4195	0	166	518	4879

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	4642
X-RAY DIFFRACTION	f_angle_d	0.892	6382
X-RAY DIFFRACTION	f_dihedral_angle_d	11.348	2839
X-RAY DIFFRACTION	f_chiral_restr	0.048	741
X-RAY DIFFRACTION	f_plane_restr	0.005	828

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 (%)
1.73-1.7497	0.3659	211	0.3268	3904	X-RAY DIFFRACTION	99
1.7497-1.7703	0.3296	221	0.3116	3886	X-RAY DIFFRACTION	99
1.7703-1.7918	0.342	212	0.3135	4075	X-RAY DIFFRACTION	99
1.7918-1.8145	0.3479	210	0.3107	3949	X-RAY DIFFRACTION	99
1.8145-1.8384	0.3542	203	0.2971	3928	X-RAY DIFFRACTION	99
1.8384-1.8636	0.3306	236	0.3012	3907	X-RAY DIFFRACTION	99
1.8636-1.8902	0.3508	198	0.3252	3754	X-RAY DIFFRACTION	96
1.8902-1.9184	0.3977	213	0.3269	3769	X-RAY DIFFRACTION	93
1.9184-1.9484	0.3347	193	0.3191	3601	X-RAY DIFFRACTION	91
1.9484-1.9803	0.2908	204	0.286	3799	X-RAY DIFFRACTION	94
1.9803-2.0145	0.3023	187	0.2672	3704	X-RAY DIFFRACTION	94
2.0145-2.0511	0.2835	195	0.2661	3825	X-RAY DIFFRACTION	97
2.0511-2.0906	0.2836	201	0.2537	3674	X-RAY DIFFRACTION	92
2.0906-2.1332	0.2866	205	0.2301	3900	X-RAY DIFFRACTION	98
2.1332-2.1796	0.304	209	0.2154	3937	X-RAY DIFFRACTION	99
2.1796-2.2303	0.2533	209	0.2137	3964	X-RAY DIFFRACTION	98
2.2303-2.2861	0.2318	206	0.2005	3787	X-RAY DIFFRACTION	95
2.2861-2.3479	0.2056	204	0.1738	3850	X-RAY DIFFRACTION	99
2.3479-2.4169	0.2196	203	0.1721	3902	X-RAY DIFFRACTION	99
2.4169-2.4949	0.2002	207	0.1703	3962	X-RAY DIFFRACTION	98
2.4949-2.5841	0.1949	196	0.1605	3710	X-RAY DIFFRACTION	95
2.5841-2.6875	0.1873	195	0.1688	3761	X-RAY DIFFRACTION	96
2.6875-2.8098	0.2141	204	0.1668	3926	X-RAY DIFFRACTION	97
2.8098-2.9579	0.2141	208	0.1669	3925	X-RAY DIFFRACTION	98
2.9579-3.1431	0.2054	206	0.1695	3851	X-RAY DIFFRACTION	97
3.1431-3.3856	0.1969	199	0.1631	3818	X-RAY DIFFRACTION	96
3.3856-3.726	0.2197	194	0.1582	3547	X-RAY DIFFRACTION	89
3.726-4.2645	0.1572	196	0.1451	3654	X-RAY DIFFRACTION	92
4.2645-5.3701	0.1757	203	0.1269	3746	X-RAY DIFFRACTION	94
5.3701-36.581	0.1707	202	0.151	3862	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	0.5094	-0.2522	0.1085	1.0109	-0.2095	0.4041	0.0329	-0.0462	-0.0023	0.1845	-0.1183	-0.1389	0.0528	0.0809	-0.0138	0.1707	-0.0188	-0.019	0.1478	0.0433	0.1734	23.8789	-11.7438	23.5233
2	0.4349	0.3533	0.2253	1.4275	-0.2614	0.6701	-0.0276	0.0166	-0.0332	-0.0312	-0.0979	-0.2887	-0.0425	0.1271	0	0.1833	-0.0188	0.0059	0.1624	0.0449	0.2125	26.8372	-7.1848	16.0637
3	0.6661	0.2965	0.4057	0.3456	-0.2865	0.3633	0.0155	0.1059	-0.1058	0.0047	-0.0951	-0.1559	0.0521	0.1477	-0.0047	0.1612	-0.0148	0.0085	0.1681	0.023	0.171	14.3667	3.6083	5.2564
4	1.1412	0.2642	0.5131	0.9889	-1.4349	1.6791	0.0387	-0.0414	0.0244	-0.034	0.0075	0.1292	0.0641	-0.0993	0.0017	0.1348	-0.0092	-0.009	0.1439	0.0083	0.139	4.5739	1.1991	4.9372
5	1.048	-0.6557	0.0727	0.8529	0.173	0.7512	-0.0292	0.231	-0.1917	-0.0388	-0.0663	0.1179	0.0451	-0.001	-0.0407	0.115	0.0029	0.0364	0.1657	-0.0477	0.1727	39.1758	-2.7564	-26.4202
6	0.4747	-0.4383	0.0266	0.4266	0.4722	0.6327	-0.0733	0.0014	-0.3215	0.0766	-0.0435	0.0758	0.1064	-0.0778	-0.0009	0.1646	0.0124	0.0523	0.1787	-0.0082	0.2477	35.053	-5.5139	-18.4988
7	0.0876	0.1528	0.0176	0.1875	0.0619	0.177	-0.1363	-0.303	-0.2247	0.1797	-0.0262	0.2362	0.0945	-0.1649	-0.0084	0.221	0.0455	0.0612	0.2617	0.028	0.2033	41.4333	-7.7408	-10.1752
8	0.2588	-0.3259	0.1353	0.1948	0.0393	0.264	-0.1891	0.0353	-0.1593	0.1244	-0.0984	-0.0725	0.0273	-0.1474	-0.0045	0.1608	-0.0032	0.039	0.2253	-0.0224	0.239	29.2471	0.8044	-16.383
9	0.1319	0.122	0.0922	0.1112	0.023	0.1219	0.0327	0.4598	0.1125	-0.1051	-0.0757	0.0871	-0.0857	-0.2919	0.0001	0.2045	0.024	-0.0198	0.3645	-0.0721	0.1923	28.9275	3.1919	-31.4024
10	0.7002	0.1097	-0.307	0.5318	0.6534	0.4567	-0.0102	0.0473	-0.1324	0.1546	-0.1002	-0.0136	0.1858	-0.0035	-0.0052	0.1661	-0.0174	0.017	0.1842	-0.0033	0.1573	30.9111	13.1603	-8.2045
11	1.0596	-0.0059	-1	0.2667	0.5139	1.1383	-0.0358	0.0082	0.1719	-0.0891	0.1839	-0.1889	-0.1413	0.2637	0.0118	0.1461	-0.0132	-0.0005	0.1826	-0.0341	0.1568	42.1939	21.2484	-9.8831
12	0.7244	-0.008	-0.5927	0.7704	0.3579	0.5518	0.074	0.097	0.1737	-0.0486	-0.1217	0.0469	0.251	-0.0121	-0.0001	0.1967	0.0158	-0.0078	0.1951	-0.0288	0.1496	31.6853	19.2469	-5.5001

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 2 through 59 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 60 through 158 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 159 through 199 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 200 through 268 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 2 through 59 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 60 through 106 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 107 through 119 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 120 through 140 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 141 through 158 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 159 through 199 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 200 through 238 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 239 through 269 )

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