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

ID or keywords:

Entry

Database: PDB / ID: 5igt

Title

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

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 /

ERYTHROMYCIN A /

GUANOSINE / Macrolide 2'-phosphotransferase

Function and homology information

Biological species

Escherichia coli (E. coli)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

FOURIER SYNTHESIS / Resolution: 1.39 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	5igt.cif.gz	200.5 KB	Display	PDBx/mmCIF format
PDB format	pdb5igt.ent.gz	162.7 KB	Display	PDB format
PDBx/mmJSON format	5igt.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/ig/5igt ftp://data.pdbj.org/pub/pdb/validation_reports/ig/5igt	HTTPS FTP

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Related structure data

Related structure data	5ighC 5igiC 5igjC 5igpC 5igrSC 5igsC 5iguC 5igvC 5igwC 5igyC 5igzC 5ih0C 5ih1C 5iwuC C: citing same article (ref.) S: Starting model for refinement
Similar structure data	5igi-d 5igp-d 5yw4-d 5igr-d 5igs-d 6ggh-1 5igj-d 4b45-d 5igw-d 5qfi-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	#82 - Oct 2006 Cytochrome p450 similarity (1) #121 - Jan 2010 70S Ribosomes similarity (1) #146 - Feb 2012 Aminoglycoside Antibiotics similarity (2)

Deposited unit

A: Macrolide 2'-phosphotransferase

hetero molecules

34.4 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
68.8 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	45.270, 45.270, 247.050
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	154
Space group name H-M	P3₂21

Components on special symmetry positions

ID	Model	Components
1	1	A-526- 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: 33266.828 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: Tf481A 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-GMP / GUANOSINE / Guanosine Mass: 283.241 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₀H₁₃N₅O₅
#3: Chemical	ChemComp-ERY / ERYTHROMYCIN A / Erythromycin Mass: 733.927 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃₇H₆₇NO₁₃ / Comment: antibiotic*YM
#4: Chemical	ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₄H₁₂NO₃ / Comment: pH buffer*YM
#5: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 403 / 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: 2.21 Å³/Da / Density % sol: 44.28 %
Crystal grow	Temperature: 295 K / Method: vapor diffusion / pH: 6.2 Details: 0.1M Na citrate, pH 6.2, 15% isopropanol, 33% 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: 1.39→39.205 Å / Num. obs: 60813 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 6.6 % / R_merge(I) obs: 0.028 / Net I/σ(I): 31.61

Reflection shell

Resolution (Å)	Highest resolution (Å)	R_merge(I) obs	Mean I/σ(I) obs	Diffraction-ID	% possible all
1.39-1.43		0.559	2.15	1	98.9
1.43-1.47		0.443	3.1	1	99.9
1.47-1.51		0.364	4.6	1	100
1.51-1.55		0.302	6.5	1	100
1.55-1.61		0.241	8.18	1	100
1.61-1.66		0.194	10.07	1	100
1.66-1.72		0.153	12.91	1	100
1.72-1.79		0.12	16.37	1	100
1.79-1.87		0.097	20.14	1	100
1.87-1.97		0.072	26.85	1	100
1.97-2.07		0.054	35.06	1	100
2.07-2.2		0.041	44.57	1	100
2.2-2.35		0.034	52.68	1	100
2.35-2.54		0.03	58.37	1	99.9
2.54-2.78		0.026	67.32	1	99.9
2.78-3.11		0.02	81.75	1	99.8
3.11-3.59		0.015	99.82	1	99.7
3.59-4.4		0.012	111.78	1	99.7
4.4-6.22		0.012	111.6	1	99.6
	6.22	0.012	112.88	1	98.1

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Processing

Software

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

Refinement

Method to determine structure:

FOURIER SYNTHESIS
Starting model: 5IGR

5igr

Resolution: 1.39→39.205 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 14.85

	R_factor	Num. reflection	% reflection
R_free	0.1649	3026	4.98 %
R_work	0.1512	-	-
obs	0.1519	60813	99.84 %

Solvent computation

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

Displacement parameters

B_iso max: 67.99 Å² / B_iso mean: 17.81 Å² / B_iso min: 5.8 Å²

Refinement step

Cycle: final / Resolution: 1.39→39.205 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2334	0	159	403	2896
B_iso mean	-	-	19.1	28.14	-
Num. residues	-	-	-	-	300

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.01	2556
X-RAY DIFFRACTION	f_angle_d	1.318	3512
X-RAY DIFFRACTION	f_chiral_restr	0.068	406
X-RAY DIFFRACTION	f_plane_restr	0.007	446
X-RAY DIFFRACTION	f_dihedral_angle_d	11.951	901

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 22

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
1.3899-1.4116	0.2763	135	0.2412	2608	2743	99
1.4116-1.4348	0.2391	130	0.2233	2482	2612	99
1.4348-1.4595	0.2162	139	0.2028	2659	2798	100
1.4595-1.486	0.2245	129	0.1864	2515	2644	100
1.486-1.5146	0.2163	135	0.1874	2627	2762	100
1.5146-1.5455	0.197	135	0.1702	2543	2678	100
1.5455-1.5792	0.1774	135	0.1553	2598	2733	100
1.5792-1.6159	0.1767	139	0.1525	2643	2782	100
1.6159-1.6563	0.1865	130	0.1537	2531	2661	100
1.6563-1.7011	0.1531	140	0.1498	2625	2765	100
1.7011-1.7511	0.1871	137	0.1517	2600	2737	100
1.7511-1.8077	0.1955	138	0.1473	2611	2749	100
1.8077-1.8723	0.1524	137	0.1495	2614	2751	100
1.8723-1.9472	0.1627	137	0.1455	2598	2735	100
1.9472-2.0358	0.1445	137	0.1422	2614	2751	100
2.0358-2.1432	0.1497	141	0.1362	2645	2786	100
2.1432-2.2774	0.1404	141	0.1325	2617	2758	100
2.2774-2.4532	0.1535	139	0.1361	2668	2807	100
2.4532-2.7001	0.1439	140	0.1476	2672	2812	100
2.7001-3.0906	0.1707	141	0.153	2676	2817	100
3.0906-3.8933	0.1679	144	0.1392	2729	2873	100
3.8933-39.2206	0.1589	147	0.162	2912	3059	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	5.7236	0.594	1.5696	3.5526	-1.3057	4.2734	-0.0771	-0.1913	0.7992	-0.1671	0.0285	0.3458	-0.2822	-0.2145	-0.0002	0.2648	-0.1071	-0.0147	0.2819	0.0077	0.2509	36.9521	54.3126	293.4394
2	3.9632	-2.1886	2.4598	4.9733	-0.1301	6.3778	-0.2811	-0.3024	0.5985	0.7683	-0.0692	-0.4752	-0.9235	0.1794	0.2173	0.3501	-0.0237	-0.0398	0.168	-0.0249	0.275	29.3897	59.947	284.1083
3	1.1221	-0.6872	0.9376	2.6428	-1.9241	4.2105	-0.0039	-0.0491	0.0158	0.4951	0.2216	-0.0848	-0.5989	-0.4795	-0.1791	0.3388	0.0633	0.0006	0.1646	-0.0089	0.1566	22.0499	57.9283	282.7428
4	6.3344	-3.2697	-2.8228	3.8548	2.3149	2.7388	-0.4337	-0.3839	-0.0865	0.27	-0.0527	-0.3688	-0.1318	0.0183	0.3292	0.2242	0.041	-0.049	0.3642	0.028	0.2125	31.394	47.6025	285.2902
5	3.2875	0.2742	-2.2958	1.4427	-0.1687	3.8125	0.0927	-0.0915	0.0634	-0.0763	-0.076	-0.4033	-0.1831	0.3391	0.0056	0.1739	0.0108	0.0296	0.2046	0.0343	0.2184	32.6763	49.1302	278.8308
6	4.2369	-0.2934	-1.2972	4.0353	-0.0762	4.5275	-0.2989	-0.0817	0.0347	0.4722	0.3077	0.6224	0.0504	-0.3969	-0.0482	0.1851	0.019	0.0258	0.2122	0.0073	0.1868	18.2774	49.4471	283.0505
7	1.8124	0.7602	-1.7111	1.2506	-1.079	3.3417	-0.182	-0.1614	-0.2116	-0.2326	-0.1215	-0.3619	0.2514	0.2229	0.287	0.1554	-0.008	0.0263	0.1706	0.0099	0.1805	34.2163	52.8405	270.5615
8	3.7549	2.3054	1.4796	4.473	0.5716	2.3042	-0.0875	-0.0065	-0.0668	0.1716	0.1635	-0.0278	-0.0922	0.1662	-0.0994	0.1546	0.0273	0.0062	0.1483	-0.0221	0.116	22.4055	46.8337	262.8541
9	0.747	0.4148	-0.4841	1.3851	0.3947	0.9383	0.0184	0.0315	0.078	0.014	-0.063	0.2025	-0.0288	-0.097	0.0386	0.0871	0.006	-0.0095	0.1144	-0.004	0.0963	20.5979	44.4155	273.111
10	6.1827	0.0062	-0.9063	2.4912	-0.2682	3.2585	0.0731	-0.3374	1.05	0.0294	-0.1293	-0.1049	-0.2565	0.4517	0.0119	0.1286	0.0078	-0.0067	0.1589	-0.0008	0.1768	34.2185	31.3812	282.4931
11	0.8737	0.0156	-0.0117	0.8351	-0.1003	1.8651	0.0103	-0.0836	-0.1126	0.037	0.0047	0.0594	0.2658	-0.1779	0.0041	0.0864	-0.0184	-0.0004	0.089	0.0088	0.0985	21.113	26.331	267.2023
12	1.7708	-0.4683	-0.0028	0.5379	0.2835	0.6876	0.0934	0.073	-0.0057	-0.1043	-0.0686	-0.0094	-0.077	0.0684	-0.0075	0.081	0.0039	-0.0063	0.1286	0.0213	0.0699	27.6784	38.821	251.0196
13	4.2101	1.1152	1.0809	2.5753	0.048	0.3144	-0.0272	0.4373	-0.015	-0.2321	-0.2055	-0.1184	0.0056	0.4949	0.0893	0.0625	0.0038	0.0072	0.2475	0.0564	0.1071	46.2093	36.5755	254.0291
14	1.6882	-0.037	-0.0588	3.9448	1.2483	2.3617	-0.0912	0.437	-0.207	-0.0601	0.2062	-0.1273	-0.0265	0.4004	-0.0554	0.077	-0.0013	-0.0235	0.2125	-0.0178	0.1824	54.353	30.6466	259.2282
15	1.0837	-0.1848	0.0611	1.008	-0.0294	0.7813	0.0342	0.1539	-0.1046	-0.1074	-0.0376	-0.1207	0.0289	0.0549	0.0091	0.0774	-0.0102	0.0097	0.1073	-0.0065	0.0922	37.2349	27.2454	254.1295
16	2.2008	0.1758	-0.4002	2.0879	-0.2447	1.7815	-0.0904	-0.1606	-0.1654	0.2636	0.0719	0.1196	0.0771	-0.079	0.0073	0.0905	-0.0098	0.013	0.1299	0.0244	0.0842	22.3242	30.3994	276.5168
17	0.3084	-0.0821	-0.1187	0.5774	0.0469	0.484	-0.0014	-0.0276	-0.0596	0.025	-0.0331	-0.0558	0.0149	0.1095	0.0314	0.0526	0.0024	-0.0068	0.0917	0.0068	0.0712	30.2571	31.2796	264.9461
18	8.2073	-1.7537	3.3315	2.8409	-0.9196	4.6505	0.1214	-0.2283	-0.4365	-0.0728	0.0441	-0.2626	0.5262	0.0759	-0.0853	0.1177	0.008	0.0175	0.1182	0.0265	0.2062	27.7104	16.7739	266.1953
19	1.8466	0.3922	-0.2906	0.5011	-0.0862	0.5568	-0.012	0.1465	0.0069	-0.0443	0.0238	0.0335	0.0002	0.0315	-0.0033	0.084	0.0086	-0.0013	0.1202	0.0014	0.105	34.7236	27.5585	259.9468
20	2.4906	-0.9257	-0.5294	5.1298	0.7119	2.9181	0.0718	-0.3611	0.0171	0.302	0.15	-0.1203	0.1389	0.0735	-0.1533	0.102	-0.0219	-0.0278	0.2066	0.0065	0.1405	51.3065	34.831	268.7783

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	(chain A and resid 2:7)	A	2 - 7
2	X-RAY DIFFRACTION	2	(chain A and resid 8:15)	A	8 - 15
3	X-RAY DIFFRACTION	3	(chain A and resid 16:26)	A	16 - 26
4	X-RAY DIFFRACTION	4	(chain A and resid 27:30)	A	27 - 30
5	X-RAY DIFFRACTION	5	(chain A and resid 31:43)	A	31 - 43
6	X-RAY DIFFRACTION	6	(chain A and resid 44:50)	A	44 - 50
7	X-RAY DIFFRACTION	7	(chain A and resid 51:61)	A	51 - 61
8	X-RAY DIFFRACTION	8	(chain A and resid 62:74)	A	62 - 74
9	X-RAY DIFFRACTION	9	(chain A and resid 75:102)	A	75 - 102
10	X-RAY DIFFRACTION	10	(chain A and resid 103:116)	A	103 - 116
11	X-RAY DIFFRACTION	11	(chain A and resid 117:139)	A	117 - 139
12	X-RAY DIFFRACTION	12	(chain A and resid 140:157)	A	140 - 157
13	X-RAY DIFFRACTION	13	(chain A and resid 158:168)	A	158 - 168
14	X-RAY DIFFRACTION	14	(chain A and resid 169:175)	A	169 - 175
15	X-RAY DIFFRACTION	15	(chain A and resid 176:201)	A	176 - 201
16	X-RAY DIFFRACTION	16	(chain A and resid 202:216)	A	202 - 216
17	X-RAY DIFFRACTION	17	(chain A and resid 217:240)	A	217 - 240
18	X-RAY DIFFRACTION	18	(chain A and resid 241:249)	A	241 - 249
19	X-RAY DIFFRACTION	19	(chain A and resid 250:284)	A	250 - 284
20	X-RAY DIFFRACTION	20	(chain A and resid 285:301)	A	285 - 301

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