PDB-5igh: Macrolide 2'-phosphotransferase type I

ID or keywords:

Entry

Database: PDB / ID: 5igh

Title

Macrolide 2'-phosphotransferase type I

Components

Macrolide 2'-phosphotransferase

Keywords

TRANSFERASE / macrolide phosphotransferase / kinase

Function / homology

Function and homology information

transferase activity
Similarity search - Function

Biological species

Escherichia coli (E. coli)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MAD / Resolution: 1.55 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	Oct 16, 2024	Group: Data collection / Database references / Structure summary Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5igh.cif.gz	205.7 KB	Display	PDBx/mmCIF format
PDB format	pdb5igh.ent.gz	171.5 KB	Display	PDB format
PDBx/mmJSON format	5igh.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	5igh_validation.pdf.gz	433.3 KB	Display	wwPDB validaton report
Full document	5igh_full_validation.pdf.gz	434.9 KB	Display
Data in XML	5igh_validation.xml.gz	18.2 KB	Display
Data in CIF	5igh_validation.cif.gz	28.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ig/5igh ftp://data.pdbj.org/pub/pdb/validation_reports/ig/5igh	HTTPS FTP

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Related structure data

Related structure data	5igiC 5igjC 5igpC 5igrC 5igsC 5igtC 5iguC 5igvC 5igwC 5igyC 5igzC 5ih0C 5ih1C 5iwuC C: citing same article (ref.)
Similar structure data	4g0j-10 2dfv-3 3c3p-1 4ei8-d 4g0j-1 3gd6-d 5ih0-d 4dnh-d 4jn7-d 6nko-6 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: Macrolide 2'-phosphotransferase

hetero molecules

33.8 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
67.7 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	84.100, 84.100, 98.370
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	154
Space group name H-M	P3₂21

Components on special symmetry positions

ID	Model	Components
1	1	A-942- HOH

#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: 33641.988 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, AM267_25240, AM268_24740, AN205_25580, AN669_16770, ASU34_20250, AZ95_0038, ECONIH1_26770, ERS085366_04054, ERS085367_04848, ERS139269_04809, ERS150873_04753, ETN48_p0083, ...Gene: mphA, mph(A), mph2, AM267_25240, AM268_24740, AN205_25580, AN669_16770, ASU34_20250, AZ95_0038, ECONIH1_26770, ERS085366_04054, ERS085367_04848, ERS139269_04809, ERS150873_04753, ETN48_p0083, 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-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO₄
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 444 / Source method: isolated from a natural source / Formula: H₂O
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: 2.96 Å³/Da / Density % sol: 58.46 %
Crystal grow	Temperature: 295 K / Method: vapor diffusion / pH: 9 Details: 0.1 M bicine, 2.2 M ammonium sulfate, 5% glycerol, 3% PEG 400

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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: Jun 29, 2009
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: 1.55→19.79 Å / Num. obs: 55320 / % possible obs: 94.1 % / Observed criterion σ(I): -3 / Redundancy: 6.6 % / R_merge(I) obs: 0.043 / Net I/σ(I): 23.46
Reflection shell	Resolution: 1.55→1.59 Å / R_merge(I) obs: 0.468 / Mean I/σ(I) obs: 2.73 / % possible all: 69.1

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Phasing

Phasing	Method: MAD

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Processing

Software

Name	Version	Classification
PHENIX	DEV_1034	refinement
XSCALE		data scaling
SOLVE		phasing
PDB_EXTRACT	3.2	data extraction

Refinement

Method to determine structure:

MAD / Resolution: 1.55→19.79 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 2 / Phase error: 16.5

	R_factor	Num. reflection	% reflection
R_free	0.164	1953	3.53 %
R_work	0.151	-	-
obs	0.151	55316	94.1 %

Solvent computation

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

Displacement parameters

B_iso mean: 28.71 Å²

Refinement step

Cycle: LAST / Resolution: 1.55→19.79 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2345	0	10	444	2799

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.01	2670
X-RAY DIFFRACTION	f_angle_d	1.277	3683
X-RAY DIFFRACTION	f_dihedral_angle_d	11.59	988
X-RAY DIFFRACTION	f_chiral_restr	0.068	410
X-RAY DIFFRACTION	f_plane_restr	0.006	493

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 (%)
1.55-1.5887	0.2613	101	0.2227	2772	X-RAY DIFFRACTION	69
1.5887-1.6317	0.2462	105	0.192	3008	X-RAY DIFFRACTION	76
1.6317-1.6797	0.2237	122	0.175	3380	X-RAY DIFFRACTION	83
1.6797-1.7339	0.1879	133	0.1511	3664	X-RAY DIFFRACTION	92
1.7339-1.7958	0.1879	151	0.1447	3990	X-RAY DIFFRACTION	100
1.7958-1.8676	0.1542	145	0.148	4051	X-RAY DIFFRACTION	100
1.8676-1.9526	0.1626	147	0.1442	3998	X-RAY DIFFRACTION	100
1.9526-2.0554	0.1727	151	0.1433	4037	X-RAY DIFFRACTION	100
2.0554-2.184	0.1869	148	0.1404	4016	X-RAY DIFFRACTION	100
2.184-2.3524	0.1752	147	0.1405	4059	X-RAY DIFFRACTION	100
2.3524-2.5887	0.1594	149	0.15	4041	X-RAY DIFFRACTION	100
2.5887-2.9622	0.1862	150	0.1475	4073	X-RAY DIFFRACTION	100
2.9622-3.728	0.1495	153	0.1431	4106	X-RAY DIFFRACTION	100
3.728-19.7889	0.1384	151	0.1602	4168	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	0.0595	-0.1246	-0.0547	0.1114	0.024	0.0948	-0.0374	-0.0515	-0.023	0.2374	0.1809	-0.2591	0.0664	0.2601	-0	0.207	0.0377	-0.0159	0.2997	-0.042	0.2377	4.7262	45.0282	59.912
2	0.5899	-0.631	-0.1004	0.2854	0.058	0.4323	-0.0137	-0.2243	-0.1502	-0.0182	0.0224	0.0584	0.0769	0.1014	-0	0.1424	0.0142	0.0165	0.237	0.0355	0.1984	2.5674	39.1614	52.9161
3	0.803	-0.5863	-0.1199	0.4197	0.2726	0.2552	-0.0076	-0.1715	-0.0241	-0.0873	-0.0431	-0.0469	-0.0086	0.075	0	0.1397	-0.0019	0.0049	0.1492	0.0329	0.1888	3.9245	39.5009	47.0039
4	0.1181	-0.1015	-0.1843	0.1018	0.0775	0.1574	0.0432	0.0185	0.0195	0.0489	0.1026	0.0822	-0.0642	-0.1094	-0	0.1931	0.027	-0.005	0.2022	0.0274	0.1885	0.4628	37.9377	31.0247
5	0.2491	0.2593	-0.201	-0.0216	-0.2051	0.449	0.0783	-0.0084	-0.0189	-0.0776	0.0342	0.095	-0.0419	-0.1124	0	0.1265	0.0116	-0.0184	0.1507	0.0315	0.1762	0.2053	35.1232	40.3291
6	1.0428	-0.0139	-0.0521	0.3105	-0.2233	0.5901	0.0565	-0.1992	-0.178	0.0235	0.035	0.028	0.4079	0.1386	0.0163	0.2352	0.0591	-0.0352	0.1631	0.0131	0.1968	16.094	20.9453	40.5033
7	0.7331	-0.8784	0.375	0.6259	-0.1952	0.3833	0.1385	0.3133	0.086	-0.2485	-0.0763	0.0143	0.068	-0.0204	0.0022	0.1872	0.0334	0.0011	0.1878	0.0204	0.1486	12.194	37.3596	19.7
8	0.3003	0.0581	-0.0924	0.2678	-0.0092	0.1024	-0.1191	-0.1097	0.5451	-0.1464	0.2925	-0.0351	-0.3237	-0.0002	0.0806	0.2932	-0.0734	-0.0301	0.1344	-0.0863	0.4706	30.4738	48.1774	27.0512
9	0.0093	-0.0211	-0.0103	0.0292	0.01	0.0091	-0.0435	0.0568	0.1428	-0.1439	-0.2986	-0.2792	-0.0525	0.3245	0	0.2337	-0.0716	0.0511	0.3103	-0.0007	0.2811	39.5764	39.5924	25.7644
10	0.8439	-0.1219	0.0677	0.6178	-0.0349	-0.0508	0.1072	0.1874	-0.0083	-0.1489	-0.0396	-0.0404	0.066	0.098	0.0157	0.2008	0.0566	0.0173	0.2093	-0.0064	0.1408	23.0885	32.5576	21.7272
11	0.0117	-0.0035	-0.0096	0.0212	0.0026	0.0034	0.1901	-0.1399	-0.3604	0.2615	0.0565	0.1155	0.4217	0.0477	0.0002	0.3341	0.0292	-0.0436	0.1475	0.0636	0.3047	9.0722	15.132	39.4576
12	0.5099	0.416	-0.5033	0.2428	-0.4856	0.4077	0.0184	-0.0337	-0.0937	-0.0475	-0.0312	-0.0181	-0.0035	0.1048	0.0012	0.1135	0.0448	-0.0172	0.0894	0.0034	0.1066	15.8957	28.5101	29.746
13	0.8981	0.1266	-0.5639	0.4468	-0.133	0.9433	0.0047	0.2718	-0.3281	-0.3205	-0.0584	-0.1969	0.2042	0.281	-0.0481	0.2483	0.0741	-0.0091	0.1678	-0.0572	0.228	21.3477	22.8275	21.6147
14	0.0324	0.0529	-0.053	0.1692	-0.1001	0.1939	-0.2672	-0.7235	0.5264	0.3657	0.1235	0.2162	0.0773	-0.2563	-0.001	0.2645	0.1008	0.0579	0.3966	-0.1356	0.3203	23.5067	43.7416	33.2527
15	0.0937	-0.0721	0.0869	0.1696	-0.0968	0.1177	0.0105	-0.149	0.4399	-0.1145	-0.1613	-0.0217	0.0689	-0.1369	-0.1087	0.5263	0.265	0.0649	0.7696	-0.5994	-0.3082	28.1419	44.4526	40.8063
16	0.0277	-0.0021	0.0116	0.032	-0.0203	0.001	-0.2204	-0.3308	-0.1834	0.2016	0.1536	-0.4228	-0.1299	-0.2136	-0.0002	0.3099	0.038	-0.0356	0.4253	-0.0302	0.2864	35.8953	37.3021	32.3578

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	(CHAIN A AND RESID 1:15)
2	X-RAY DIFFRACTION	2	(CHAIN A AND RESID 16:45)
3	X-RAY DIFFRACTION	3	(CHAIN A AND RESID 46:59)
4	X-RAY DIFFRACTION	4	(CHAIN A AND RESID 60:75)
5	X-RAY DIFFRACTION	5	(CHAIN A AND RESID 76:96)
6	X-RAY DIFFRACTION	6	(CHAIN A AND RESID 97:131)
7	X-RAY DIFFRACTION	7	(CHAIN A AND RESID 132:164)
8	X-RAY DIFFRACTION	8	(CHAIN A AND RESID 165:171)
9	X-RAY DIFFRACTION	9	(CHAIN A AND RESID 172:175)
10	X-RAY DIFFRACTION	10	(CHAIN A AND RESID 176:207)
11	X-RAY DIFFRACTION	11	(CHAIN A AND RESID 208:213)
12	X-RAY DIFFRACTION	12	(CHAIN A AND RESID 214:241)
13	X-RAY DIFFRACTION	13	(CHAIN A AND RESID 242:274)
14	X-RAY DIFFRACTION	14	(CHAIN A AND RESID 275:285)
15	X-RAY DIFFRACTION	15	(CHAIN A AND RESID 286:294)
16	X-RAY DIFFRACTION	16	(CHAIN A AND RESID 295:301)

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