PDB-5igs: Macrolide 2'-phosphotransferase type I - complex with guanosine a...

ID or keywords:

Entry

Database: PDB / ID: 5igs

Title

Macrolide 2'-phosphotransferase type I - complex with guanosine and oleandomycin

Components

Macrolide 2'-phosphotransferase

Keywords

TRANSFERASE/ANTIBIOTIC / macrolide phosphotransferase / kinase / TRANSFERASE-ANTIBIOTIC complex

Function / homology

: / Aminoglycoside phosphotransferase / Phosphotransferase enzyme family / transferase activity / Protein kinase-like domain superfamily / GUANOSINE / ISOPROPYL ALCOHOL / Chem-ZIO / Aminoglycoside phosphotransferase

Function and homology information

Biological species

Escherichia coli (E. coli)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.38 Å

Authors

Berghuis, A.M. / Fong, D.H.

Funding support

Canada, 1items

Citation

Journal: Structure / Year: 2017
Title: Structural Basis for Kinase-Mediated Macrolide Antibiotic Resistance.
Authors: Fong, D.H. / Burk, D.L. / Blanchet, J. / Yan, A.Y. / Berghuis, A.M.

History

Deposition	Feb 28, 2016	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Apr 26, 2017	Provider: repository / Type: Initial release
Revision 1.1	May 3, 2017	Group: Database references
Revision 1.2	May 17, 2017	Group: Database references
Revision 1.3	Sep 13, 2017	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4	Jan 8, 2020	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5	Sep 27, 2023	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5igs.cif.gz	201 KB	Display	PDBx/mmCIF format
PDB format	pdb5igs.ent.gz	163.9 KB	Display	PDB format
PDBx/mmJSON format	5igs.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	5igs_validation.pdf.gz	1.2 MB	Display	wwPDB validaton report
Full document	5igs_full_validation.pdf.gz	1.2 MB	Display
Data in XML	5igs_validation.xml.gz	18.7 KB	Display
Data in CIF	5igs_validation.cif.gz	29.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ig/5igs ftp://data.pdbj.org/pub/pdb/validation_reports/ig/5igs	HTTPS FTP

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Related structure data

Related structure data	5ighC 5igiC 5igjC 5igpC 5igrSC 5igtC 5iguC 5igvC 5igwC 5igyC 5igzC 5ih0C 5ih1C 5iwuC C: citing same article (ref.) S: Starting model for refinement
Similar structure data	5igj-d 5igp-d 5z2x-2 5qfi-d 5igt-d 5yw4-d 5ih0-d 5zec-2 1tg5-d 5ih1-d 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) #70 - Oct 2005 Designer Proteins similarity (1)

Deposited unit

A: Macrolide 2'-phosphotransferase

hetero molecules

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

1

Idetical with deposited unit
defined by author

2

A: Macrolide 2'-phosphotransferase

hetero molecules

A: Macrolide 2'-phosphotransferase

hetero molecules

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

Unit cell

Length a, b, c (Å)	45.170, 45.170, 247.140
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	154
Space group name H-M	P3₂21

#1: Protein	Macrolide 2'-phosphotransferase / Macrolide 2'-phosphotransferase I / Macrolide 2'-phosphotransferase I Mph(A) / Macrolide 2'- ...Macrolide 2'-phosphotransferase I / Macrolide 2'-phosphotransferase I Mph(A) / Macrolide 2'-phosphotransferase Mph(A) / Macrolide 2-phosphotransferase / Macrolide 2-phosphotransferase protein / macrolide resistance protein / Macrolide-phosphotransferase / mph(A) / Mph(A) / Mph(A) macrolide 2'-phosphotransferase I / Uncharacterized protein Mass: 33266.828 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) Gene: mphA, mph(A), mph2, AL500_00070, AL500_01375, AL500_26825, AL500_27285, AM267_25240, AM268_24740, AN205_25580, AN669_16770, APT94_14590, APU01_18860, APU07_01730, APU10_01345, APU12_00980, ...Gene: mphA, mph(A), mph2, AL500_00070, AL500_01375, AL500_26825, AL500_27285, AM267_25240, AM268_24740, AN205_25580, AN669_16770, APT94_14590, APU01_18860, APU07_01730, APU10_01345, APU12_00980, APZ14_31330, ASU34_20250, AUO99_00035, AZ95_0038, BN3204_920003, ECONIH1_26770, ERS085366_04054, ERS085367_04848, ERS139269_04809, ERS150873_04753, ETN48_p0083, FH07_00510, orf00017, pCTXM123_C0996_11, pKC394-009, SK74_04859, SK86_03516, UN86_19875 Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q47396
#2: Chemical	ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL Mass: 60.095 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃H₈O / Comment: alkaloid*YM
#3: Chemical	ChemComp-ZIO / (3S,5R,6S,7R,8R,11R,12S,13R,14S,15S)-6-HYDROXY-5,7,8,11,13,15-HEXAMETHYL-4,10-DIOXO-14-{[3,4,6-TRIDEOXY-3-(DIMETHYLAMINO)-BETA-D-XYLO-HEXOPYRANOSYL]OXY}-1,9-DIOXASPIRO[2.13]HEXADEC-12-YL 2,6-DIDEOXY-3-O-METHYL-ALPHA-L-ARABINO-HEXOPYRANOSIDE / OLEANDOMYCIN Mass: 687.858 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃₅H₆₁NO₁₂ / Comment: antibiotic*YM
#4: Chemical	ChemComp-GMP / GUANOSINE Mass: 283.241 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₀H₁₃N₅O₅
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 438 / 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: 2.2 Å³/Da / Density % sol: 44.05 %
Crystal grow	Temperature: 295 K / Method: vapor diffusion / pH: 6.2 / Details: 0.1 M Na citrate, 15% isopropanol, 27% PEG 4000

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

CLSI

/ Beamline: 08ID-1 / Wavelength: 0.9793 Å

Detector

Type: RAYONIX MX-225 / Detector: CCD / Date: Oct 13, 2010

Radiation

Monochromator: DCM / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.9793 Å / Relative weight: 1

Reflection

Resolution: 1.38→39.118 Å / Num. obs: 59173 / % possible obs: 95.5 % / Observed criterion σ(I): -3 / Redundancy: 5.4 % / R_merge(I) obs: 0.028 / Net I/σ(I): 27.51

Reflection shell

Resolution (Å)	Highest resolution (Å)	R_merge(I) obs	Mean I/σ(I) obs	Diffraction-ID	% possible all
1.38-1.42		0.477	2.15	1	71.7
1.42-1.45		0.414	2.74	1	80.4
1.45-1.5		0.31	4.09	1	89.3
1.5-1.54		0.247	5.95	1	97.4
1.54-1.59		0.199	8.05	1	100
1.59-1.65		0.164	9.79	1	100
1.65-1.71		0.129	12.61	1	100
1.71-1.78		0.102	16.27	1	99.9
1.78-1.86		0.083	20.27	1	100
1.86-1.95		0.065	26.2	1	99.9
1.95-2.06		0.05	33.3	1	99.9
2.06-2.18		0.04	41.51	1	99.8
2.18-2.33		0.034	47.6	1	99.8
2.33-2.52		0.03	52.02	1	99.8
2.52-2.76		0.027	56.76	1	99.6
2.76-3.09		0.022	64.95	1	99.8
3.09-3.56		0.019	72.42	1	99.8
3.56-4.36		0.016	77.02	1	99.7
4.36-6.17		0.014	76.84	1	99.7
	6.17	0.015	72.74	1	96.9

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Processing

Software

Name	Version	Classification
PHENIX	1.8_1069	refinement
XDS		data reduction
XSCALE		data scaling
PHENIX		phasing
PDB_EXTRACT	3.2	data extraction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 5IGR

5igr

Resolution: 1.38→39.118 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 2.02 / Phase error: 16.17 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1665	2956	5 %
R_work	0.1547	-	-
obs	0.1553	59173	95.51 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.38→39.118 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2334	0	72	438	2844

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.01	2555
X-RAY DIFFRACTION	f_angle_d	1.343	3509
X-RAY DIFFRACTION	f_dihedral_angle_d	11.755	915
X-RAY DIFFRACTION	f_chiral_restr	0.127	405
X-RAY DIFFRACTION	f_plane_restr	0.007	450

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 (%)
1.38-1.4026	0.267	105	0.2644	1940	X-RAY DIFFRACTION	70
1.4026-1.4268	0.305	108	0.2475	2057	X-RAY DIFFRACTION	75
1.4268-1.4528	0.2618	120	0.224	2280	X-RAY DIFFRACTION	82
1.4528-1.4807	0.2319	120	0.2063	2361	X-RAY DIFFRACTION	87
1.4807-1.5109	0.2244	133	0.1997	2613	X-RAY DIFFRACTION	93
1.5109-1.5438	0.2024	140	0.1793	2688	X-RAY DIFFRACTION	99
1.5438-1.5797	0.1886	143	0.1693	2761	X-RAY DIFFRACTION	100
1.5797-1.6192	0.2064	149	0.1681	2789	X-RAY DIFFRACTION	100
1.6192-1.663	0.1934	146	0.1684	2780	X-RAY DIFFRACTION	100
1.663-1.7119	0.1791	147	0.1628	2739	X-RAY DIFFRACTION	100
1.7119-1.7672	0.2113	143	0.1607	2750	X-RAY DIFFRACTION	100
1.7672-1.8303	0.1842	148	0.1647	2804	X-RAY DIFFRACTION	100
1.8303-1.9036	0.2036	150	0.1579	2772	X-RAY DIFFRACTION	100
1.9036-1.9902	0.181	147	0.1563	2792	X-RAY DIFFRACTION	100
1.9902-2.0952	0.1664	147	0.1466	2802	X-RAY DIFFRACTION	100
2.0952-2.2264	0.1336	148	0.1381	2799	X-RAY DIFFRACTION	100
2.2264-2.3983	0.1578	150	0.1368	2816	X-RAY DIFFRACTION	100
2.3983-2.6396	0.1593	150	0.1468	2843	X-RAY DIFFRACTION	100
2.6396-3.0214	0.1601	148	0.1524	2874	X-RAY DIFFRACTION	100
3.0214-3.8062	0.1408	146	0.1407	2888	X-RAY DIFFRACTION	100
3.8062-39.1341	0.156	168	0.1565	3069	X-RAY DIFFRACTION	99

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	5.0892	-0.057	0.2032	3.2796	-1.9749	1.2041	0.0806	-0.1241	0.2334	0.0194	-0.0543	0.2554	-0.2199	-0.0573	0.0635	0.2933	-0.1175	-0.0165	0.3118	0.0025	0.2626	37.007	54.0166	293.589
2	3.976	-1.2281	1.3636	2.9978	-0.8619	5.4988	-0.0657	-0.1956	0.4355	0.4615	0.0238	-0.3398	-0.9587	0.0417	-0.0073	0.353	0.0058	-0.0298	0.1279	-0.0197	0.2368	27.2051	60.2404	281.8617
3	3.4399	0.0431	0.7	3.8531	-3.2177	2.8469	0.3226	-0.097	0.0823	0.7166	0.2695	-0.0621	-0.0348	-0.0717	-0.3322	0.373	0.0946	-0.0218	0.2338	-0.014	0.152	22.2072	54.6246	287.3011
4	1.9029	0.3393	-2.4713	1.6666	-1.3825	4.2926	-0.0558	-0.5917	-0.0142	0.0059	-0.2762	-0.6509	0.2391	0.6652	0.2881	0.206	-0.0116	-0.0095	0.4079	0.0968	0.2729	35.6439	47.7456	278.7947
5	2.2765	0.4241	-0.3178	1.8561	-0.2418	2.1118	-0.076	0.3432	-0.1309	0.0712	0.0351	0.3677	-0.2546	-0.6239	0.0893	0.1584	0.0549	0.0144	0.2668	0.0364	0.1797	21.0256	50.0001	284.0519
6	3.3774	1.1427	-2.402	1.3513	-0.9638	2.6471	-0.1771	-0.1169	-0.1998	-0.0147	-0.071	-0.274	0.1126	0.2217	0.1869	0.1338	-0.0091	-0.0006	0.2063	0.0013	0.1531	30.7323	51.0812	274.4375
7	4.1218	3.4524	1.5076	4.5051	0.8022	1.2485	0.0041	0.0854	0.0804	0.0239	0.0535	0.0367	-0.1316	0.0243	-0.0521	0.1504	0.0065	0.0185	0.1665	-0.0064	0.1311	23.3963	47.5716	263.1604
8	0.6971	0.1152	-0.4264	1.1592	0.2408	0.8431	0.0042	0.0527	0.0678	-0.022	-0.0202	0.1836	-0.0189	-0.1528	-0.0009	0.0759	0.0064	-0.0098	0.1316	0.0087	0.104	20.4113	44.7027	273.2116
9	4.8706	1.4946	-0.2348	3.1295	1.0344	1.8754	0.3394	-0.0338	1.1219	-0.0653	-0.0716	-0.5017	-0.5106	0.5719	-0.1921	0.1931	-0.0609	-0.0093	0.2974	-0.0088	0.3872	36.5617	34.6829	282.9164
10	0.9688	-0.3536	0.2903	0.6846	-0.0529	1.6613	0.0317	-0.1259	-0.0698	0.042	-0.0067	0.0484	0.3096	-0.1031	0.0084	0.1029	-0.0251	-0.0009	0.1147	0.0112	0.1052	23.7531	26.2769	271.4048
11	1.3679	-0.5612	-0.0804	0.7138	0.28	0.7147	0.0491	0.0931	0.0229	-0.0804	-0.0413	-0.0108	-0.109	0.0809	-0.0095	0.0829	-0.0056	-0.0145	0.1489	0.0252	0.0842	27.322	38.9917	251.3663
12	3.1455	0.7269	1.8076	0.1662	0.4166	1.0401	-0.1477	0.4199	0.246	-0.1241	-0.0366	-0.1295	-0.18	0.5583	0.1182	0.0933	-0.0219	-0.0024	0.2549	0.053	0.1374	47.24	37.2037	254.5259
13	2.4531	0.8068	1.1533	0.3775	0.5189	1.3726	0.2228	0.3101	-0.1894	0.0132	0.056	-0.2495	0.1701	0.3052	-0.2429	0.1036	0.0077	-0.0031	0.1666	-0.0189	0.1804	48.5097	25.4961	255.3749
14	0.7008	0.0182	-0.3626	0.7528	0.2639	0.863	0.0001	-0.0395	-0.0759	0.0129	-0.0078	0.0245	0.0302	0.0459	-0.0017	0.0536	-0.0109	-0.0142	0.1221	0.0065	0.0784	28.322	30.4932	264.8963
15	6.3168	-0.7356	2.5198	2.4632	-0.6761	3.5618	0.0626	-0.355	-0.5386	0.0938	0.1109	-0.1808	0.3572	-0.0148	-0.1615	0.1346	-0.0176	-0.0086	0.1776	0.0363	0.227	27.1899	16.81	266.0776
16	1.7424	0.3022	-0.3425	0.6031	-0.1979	0.5206	0.0457	0.0865	0.0263	-0.0554	-0.0348	0.0285	-0.0448	-0.0003	-0.0088	0.0779	-0.0069	-0.0057	0.1275	0.0038	0.1082	34.9637	27.867	260.1861
17	2.7403	0.4789	-0.1229	6.0652	1.1452	2.9474	0.153	-0.4916	-0.0059	0.3861	0.1971	-0.0691	0.1168	-0.0751	-0.2461	0.1028	-0.0243	-0.023	0.2379	0.032	0.1411	50.9937	33.3511	268.5815

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	(chain A and resid 2:7)
2	X-RAY DIFFRACTION	2	(chain A and resid 8:20)
3	X-RAY DIFFRACTION	3	(chain A and resid 21:27)
4	X-RAY DIFFRACTION	4	(chain A and resid 28:37)
5	X-RAY DIFFRACTION	5	(chain A and resid 38:47)
6	X-RAY DIFFRACTION	6	(chain A and resid 48:59)
7	X-RAY DIFFRACTION	7	(chain A and resid 60:74)
8	X-RAY DIFFRACTION	8	(chain A and resid 75:102)
9	X-RAY DIFFRACTION	9	(chain A and resid 103:110)
10	X-RAY DIFFRACTION	10	(chain A and resid 111:139)
11	X-RAY DIFFRACTION	11	(chain A and resid 140:156)
12	X-RAY DIFFRACTION	12	(chain A and resid 157:170)
13	X-RAY DIFFRACTION	13	(chain A and resid 171:185)
14	X-RAY DIFFRACTION	14	(chain A and resid 186:240)
15	X-RAY DIFFRACTION	15	(chain A and resid 241:249)
16	X-RAY DIFFRACTION	16	(chain A and resid 250:285)
17	X-RAY DIFFRACTION	17	(chain A and resid 286:301)

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