PDB-5igr: Macrolide 2'-phosphotransferase type I - complex with GDP and ole...

ID or keywords:

Entry

Database: PDB / ID: 5igr

Title

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

Components

Macrolide 2'-phosphotransferase

Keywords

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

Function / homology

Function and homology information

transferase activity
Similarity search - Function

Biological species

Escherichia coli (E. coli)

Method

X-RAY DIFFRACTION /

SYNCHROTRON / Resolution: 1.6 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	Mar 6, 2024	Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5igr.cif.gz	199.3 KB	Display	PDBx/mmCIF format
PDB format	pdb5igr.ent.gz	163.8 KB	Display	PDB format
PDBx/mmJSON format	5igr.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	5igr_validation.pdf.gz	1.1 MB	Display	wwPDB validaton report
Full document	5igr_full_validation.pdf.gz	1.1 MB	Display
Data in XML	5igr_validation.xml.gz	18.7 KB	Display
Data in CIF	5igr_validation.cif.gz	28.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ig/5igr ftp://data.pdbj.org/pub/pdb/validation_reports/ig/5igr	HTTPS FTP

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Related structure data

Related structure data	5ighC 5igiC 5igjC 5igpC 5igsC 5igtC 5iguC 5igvC 5igwC 5igyC 5igzC 5ih0C 5ih1C 5iwuC C: citing same article (ref.)
Similar structure data	5igi-d 5w86-3 5igt-d 5igy-d 6vgl-3 5yw4-d 2b7a-1 2o8j-3 6wif-4 6x8e-2 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) #135 - Mar 2011 Integrase similarity (1) #70 - Oct 2005 Designer Proteins similarity (1)

Deposited unit

A: Macrolide 2'-phosphotransferase

hetero molecules

34.5 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
69.1 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	45.110, 45.110, 246.800
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	154
Space group name H-M	P3₂21

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Protein , 1 types, 1 molecules A

#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 / Macrolide 2-phosphotransferase protein / macrolide resistance protein / Macrolide-phosphotransferase / mph(A) / Mph(A) / Mph(A) macrolide 2'-phosphotransferase I / Phosphotransferase enzyme family protein / 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, A4X18_25005, A4X18_26080, A6M24_25350, ACM48_26150, AN669_16770, APT94_14590, APZ14_31330, AZ95_0038, ECONIH1_26770, ERS085366_04054, ERS139269_04809, ERS150873_04753, ETN48_ ...Gene: mphA, mph(A), mph2, A4X18_25005, A4X18_26080, A6M24_25350, ACM48_26150, AN669_16770, APT94_14590, APZ14_31330, AZ95_0038, ECONIH1_26770, ERS085366_04054, ERS139269_04809, ERS150873_04753, ETN48_p0083, HMPREF3040_01642, orf00017, pCTXM123_C0996_11, pKC394-009, UN86_19875 Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q47396

#1: Protein

Macrolide 2'-phosphotransferase / Macrolide 2'-phosphotransferase I / Macrolide 2'-phosphotransferase I Mph(A) / Macrolide 2- ...

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, A4X18_25005, A4X18_26080, A6M24_25350, ACM48_26150, AN669_16770, APT94_14590, APZ14_31330, AZ95_0038, ECONIH1_26770, ERS085366_04054, ERS139269_04809, ERS150873_04753, ETN48_ ...
Production host:

Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q47396

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Non-polymers , 5 types, 392 molecules

#2: Chemical	ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₀H₁₅N₅O₁₁P₂ / Comment: GDP, energy-carrying molecule*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
#4: Chemical	ChemComp-NH4 / AMMONIUM ION Mass: 18.038 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: H₄N
#5: Chemical	ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL Mass: 60.095 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃H₈O
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 385 / 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: 2.19 Å³/Da / Density % sol: 43.83 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion / pH: 5.8 Details: 0.1 M Na citrate, 18% isopropanol, 27% PEG 4000, 0.2 M ammonium acetate

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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 3, 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: 1.6→39.066 Å / Num. obs: 39609 / % possible obs: 99.1 % / Observed criterion σ(I): -3 / Redundancy: 6.8 % / R_merge(I) obs: 0.04 / Net I/σ(I): 27.15

Reflection shell

Resolution (Å)	Highest resolution (Å)	R_merge(I) obs	Mean I/σ(I) obs	Diffraction-ID	% possible all
1.6-1.64		0.432	3.16	1	93.4
1.64-1.69		0.344	4.44	1	98.8
1.69-1.74		0.255	6.5	1	99.9
1.74-1.79		0.215	8.09	1	99.9
1.79-1.85		0.175	9.99	1	100
1.85-1.91		0.141	12.45	1	99.8
1.91-1.98		0.108	16.66	1	99.8
1.98-2.07		0.084	21.21	1	99.7
2.07-2.16		0.065	26.69	1	99.8
2.16-2.26		0.055	31.2	1	99.9
2.26-2.39		0.046	35.69	1	99.3
2.39-2.53		0.042	39.25	1	99.5
2.53-2.7		0.038	43.17	1	99.1
2.7-2.92		0.032	50.21	1	99.2
2.92-3.2		0.029	55.76	1	99.2
3.2-3.58		0.024	61.25	1	98.4
3.58-4.13		0.022	64.44	1	99.5
4.13-5.06		0.021	66.02	1	99.8
5.06-7.16		0.022	63.95	1	99.7
	7.16	0.022	62.46	1	97.5

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Processing

Software

Name	Version	Classification
PHENIX	dev_1627	refinement
XDS	March 5, 2012	data reduction
XSCALE		data scaling
PHENIX		phasing
PDB_EXTRACT	3.2	data extraction

Refinement

Resolution: 1.6→39.066 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 2.02 / Phase error: 16.7 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1957	2004	5.06 %
R_work	0.1572	-	-
obs	0.1591	39603	99.07 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.6→39.066 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2334	0	84	385	2803

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.016	2556
X-RAY DIFFRACTION	f_angle_d	1.662	3515
X-RAY DIFFRACTION	f_dihedral_angle_d	13.784	919
X-RAY DIFFRACTION	f_chiral_restr	0.084	406
X-RAY DIFFRACTION	f_plane_restr	0.01	448

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 (%)
1.6-1.64	0.245	127	0.2261	2459	X-RAY DIFFRACTION	93
1.64-1.6844	0.2548	138	0.2003	2619	X-RAY DIFFRACTION	99
1.6844-1.7339	0.2216	142	0.1857	2702	X-RAY DIFFRACTION	100
1.7339-1.7899	0.2424	142	0.1808	2613	X-RAY DIFFRACTION	100
1.7899-1.8539	0.2307	142	0.1783	2656	X-RAY DIFFRACTION	100
1.8539-1.9281	0.2289	140	0.1741	2650	X-RAY DIFFRACTION	100
1.9281-2.0158	0.2248	143	0.1659	2675	X-RAY DIFFRACTION	100
2.0158-2.1221	0.2285	145	0.1556	2689	X-RAY DIFFRACTION	100
2.1221-2.2551	0.2049	148	0.1498	2718	X-RAY DIFFRACTION	100
2.2551-2.4291	0.197	139	0.1478	2673	X-RAY DIFFRACTION	99
2.4291-2.6736	0.1927	144	0.1534	2697	X-RAY DIFFRACTION	99
2.6736-3.0603	0.1938	148	0.1496	2733	X-RAY DIFFRACTION	99
3.0603-3.8551	0.1747	148	0.1375	2761	X-RAY DIFFRACTION	99
3.8551-39.078	0.1656	158	0.1577	2954	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	9.5398	3.0757	-1.421	7.4916	-2.666	1.5437	0.2115	-0.3059	0.4038	0.0722	-0.1737	0.6918	-0.3089	-0.3567	0.1173	0.3199	-0.1334	-0.0334	0.3164	0.021	0.3104	37.0042	53.9503	293.1777
2	6.0179	-2.2509	1.2597	4.6307	-1.5338	5.8541	-0.1893	-0.3363	0.4911	0.5101	0.2136	-0.1631	-1.2457	-0.1512	-0.1079	0.4225	0.0499	0.012	0.217	-0.0087	0.2491	25.8992	59.6462	281.7752
3	5.3104	0.156	-4.7693	1.7454	0.0436	8.9191	-0.1866	-0.5644	-0.004	0.2082	0.0337	-0.5546	0.3227	0.9358	0.1664	0.2762	0.0435	-0.0154	0.4098	0.0778	0.2723	32.4599	48.7676	281.0499
4	2.5657	-0.9081	-1.5762	7.0406	-0.4344	5.0872	-0.0948	-0.2792	-0.0526	0.2532	0.2864	1.0484	-0.1454	-0.751	-0.0723	0.2115	0.0648	0.0097	0.4205	0.0419	0.2659	18.9576	49.6797	283.4385
5	6.3837	2.0626	-4.9111	2.8383	-2.0552	3.8793	-0.1407	-0.139	-0.6546	-0.1119	-0.1075	-0.6566	0.2169	0.5621	0.1403	0.2055	-0.0413	-0.0061	0.3514	0.0326	0.248	33.8048	52.246	271.8696
6	7.0433	5.0861	2.203	3.7159	1.6997	2.4965	0.1493	0.051	-0.09	0.0719	-0.0678	-0.0987	-0.2777	-0.1046	-0.0886	0.174	0.0111	-0.003	0.2264	-0.0006	0.1616	23.3819	47.5399	262.8446
7	1.1342	0.5222	0.5605	2.672	0.2552	1.1711	-0.0284	-0.1749	0.1393	-0.0288	-0.1015	0.5877	0.066	-0.5949	0.084	0.1018	0.0017	-0.0237	0.2981	0.0064	0.1774	16.8762	41.7376	268.3326
8	0.8329	0.3315	-0.2741	5.5349	-1.1914	1.2533	0.0255	-0.0994	0.0419	0.2498	-0.0226	0.179	-0.0238	-0.0792	-0.0051	0.1079	0.0076	-0.0145	0.2394	0.0107	0.1133	23.7035	45.0088	276.4725
9	3.8153	-0.7719	1.4925	0.6532	-0.5456	3.923	-0.0317	-0.178	0.1782	0.0601	-0.0132	0.0595	0.3007	0.0527	0.0117	0.1477	-0.0325	0.0033	0.188	0.0355	0.1458	28.2996	26.758	277.3709
10	0.501	-0.2834	-0.0148	0.3952	0.3315	0.6911	0.068	0.0093	-0.015	-0.0519	-0.0678	-0.0018	-0.1388	0.0432	-0.0051	0.131	-0.007	-0.0244	0.1834	0.0281	0.12	25.3307	37.2344	252.7662
11	4.2963	1.0239	1.849	1.4934	0.999	1.0454	0.0371	0.2581	0.4084	-0.1762	-0.145	-0.1773	-0.1893	0.4782	-0.0242	0.1279	-0.0303	0.0068	0.3402	0.0647	0.1996	48.0074	36.8897	255.1889
12	6.5247	0.9236	2.6413	1.3783	1.0056	3.5278	0.2906	0.3067	-0.4357	0.0049	-0.0434	-0.4433	0.2243	0.5534	-0.1013	0.1578	0.0219	-0.0107	0.2448	0.026	0.2392	48.5962	25.2319	255.4293
13	1.0516	-0.0704	-0.0336	1.1298	0.3049	0.7515	0.0336	-0.132	-0.1171	0.0177	-0.017	0.0292	0.0547	-0.0009	-0.0001	0.0726	-0.0329	-0.023	0.2061	0.0221	0.1209	28.0229	31.3758	264.0006
14	8.4272	1.6695	3.8895	8.0064	2.9484	5.2517	-0.0239	-0.4208	-0.7801	-0.0144	0.2109	-0.114	0.3615	0.2092	-0.2964	0.1007	-0.0106	-0.0073	0.2998	0.0848	0.2031	32.944	19.7482	269.2858
15	4.6668	0.9755	-1.1583	2.9423	-0.2055	5.3497	-0.1502	-0.0749	-0.434	-0.1499	-0.1058	0.0822	0.2204	0.0757	0.2222	0.1255	-0.029	-0.0285	0.1832	0.034	0.2271	21.6254	20.4738	260.2617
16	3.9043	2.3739	0.7589	3.145	0.8959	1.5005	0.0944	-0.0984	0.1078	-0.0488	-0.0882	0.0112	-0.0936	0.0194	-0.0452	0.1054	-0.0195	-0.0022	0.2047	0.0269	0.1493	39.901	30.3158	260.814
17	5.0647	1.1834	-0.0118	6.444	0.985	1.5693	0.0113	-0.6495	0.0365	0.2479	0.2714	0.0487	0.0681	-0.0427	-0.076	0.1403	-0.0498	-0.0196	0.3884	0.0809	0.2184	51.4329	33.7385	268.3938

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 8:23)
3	X-RAY DIFFRACTION	3	(chain A and resid 24:40)
4	X-RAY DIFFRACTION	4	(chain A and resid 41:50)
5	X-RAY DIFFRACTION	5	(chain A and resid 51:59)
6	X-RAY DIFFRACTION	6	(chain A and resid 60:74)
7	X-RAY DIFFRACTION	7	(chain A and resid 75:85)
8	X-RAY DIFFRACTION	8	(chain A and resid 86:103)
9	X-RAY DIFFRACTION	9	(chain A and resid 104:131)
10	X-RAY DIFFRACTION	10	(chain A and resid 132:157)
11	X-RAY DIFFRACTION	11	(chain A and resid 158:171)
12	X-RAY DIFFRACTION	12	(chain A and resid 172:184)
13	X-RAY DIFFRACTION	13	(chain A and resid 185:236)
14	X-RAY DIFFRACTION	14	(chain A and resid 237:245)
15	X-RAY DIFFRACTION	15	(chain A and resid 246:258)
16	X-RAY DIFFRACTION	16	(chain A and resid 259:286)
17	X-RAY DIFFRACTION	17	(chain A and resid 287:301)

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Yorodumi