PDB-5igv: Macrolide 2'-phosphotransferase type II - complex with GDP and az...

ID or keywords:

Entry

Database: PDB / ID: 5igv

Title

Macrolide 2'-phosphotransferase type II - complex with GDP and azithromycin

Components

Macrolide 2'-phosphotransferase II

Keywords

TRANSFERASE / macrolide phosphotransferase / kinase

Function / homology

Function and homology information

transferase activity / metal ion binding
Similarity search - Function

Biological species

Escherichia coli (E. coli)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

FOURIER SYNTHESIS / 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	Sep 27, 2023	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_alt_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.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_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_alt_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.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_label_atom_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

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5igv.cif.gz	211 KB	Display	PDBx/mmCIF format
PDB format	pdb5igv.ent.gz	171 KB	Display	PDB format
PDBx/mmJSON format	5igv.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	5igv_validation.pdf.gz	1.1 MB	Display	wwPDB validaton report
Full document	5igv_full_validation.pdf.gz	1.1 MB	Display
Data in XML	5igv_validation.xml.gz	19.4 KB	Display
Data in CIF	5igv_validation.cif.gz	29.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ig/5igv ftp://data.pdbj.org/pub/pdb/validation_reports/ig/5igv	HTTPS FTP

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Related structure data

Related structure data	5ighC 5igiC 5igjC 5igpC 5igrC 5igsC 5igtC 5iguC 5igwC 5igyC 5igzC 5ih0C 5ih1C 5iwuSC C: citing same article (ref.) S: Starting model for refinement
Similar structure data	5ih0-d 5o9w-d 4p47-d 6z36-1 5igw-d 2hki-d 5igs-d 5oyc-2 3pus-1 4yr7-2 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 II

hetero molecules

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

1

Idetical with deposited unit
defined by author

Unit cell

Length a, b, c (Å)	40.230, 80.450, 96.430
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

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Protein , 1 types, 1 molecules A

#1: Protein	Macrolide 2'-phosphotransferase II / Macrolide 2'-phosphotransferase II protein MphB / Macrolide 2-phosphotransferase / mph(B) Mass: 34527.211 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: mphB, pO103_99 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O32553

#1: Protein

Macrolide 2'-phosphotransferase II / Macrolide 2'-phosphotransferase II protein MphB / Macrolide 2-phosphotransferase / mph(B)

Mass: 34527.211 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Escherichia coli (E. coli) / Gene: mphB, pO103_99 / Plasmid: pET28a / Production host:

Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O32553

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Non-polymers , 5 types, 460 molecules

#2: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical	ChemComp-CA / CALCIUM ION Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: 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
#5: Chemical	ChemComp-ZIT / AZITHROMYCIN Mass: 748.984 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃₈H₇₂N₂O₁₂ / Comment: antibiotic*YM
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 456 / 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: 2.29 Å³/Da / Density % sol: 46.23 %
Crystal grow	Temperature: 295 K / Method: vapor diffusion / pH: 7.5 / Details: 0.1 M calcium acetate, 0.1M Tris, 25-40% 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-300 / Detector: CCD / Date: Feb 23, 2011
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→41.356 Å / Num. obs: 46230 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 8.1 % / R_merge(I) obs: 0.038 / Net I/σ(I): 30.01
Reflection shell	Resolution: 1.55→1.59 Å / R_merge(I) obs: 0.64 / Mean I/σ(I) obs: 3.59 / % possible all: 100

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Processing

Software

Name	Version	Classification
PHENIX	1.10PRE_2104	refinement
XSCALE		data scaling
XDS		data reduction
PHENIX		phasing
PDB_EXTRACT	3.2	data extraction

Refinement

Method to determine structure:

FOURIER SYNTHESIS
Starting model: 5IWU

5iwu

Resolution: 1.55→41.36 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 2 / Phase error: 20.85 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.209	2312	5 %
R_work	0.178	-	-
obs	0.179	46228	100 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.55→41.36 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2398	0	82	456	2936

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.009	2672
X-RAY DIFFRACTION	f_angle_d	1.128	3658
X-RAY DIFFRACTION	f_dihedral_angle_d	12.635	1576
X-RAY DIFFRACTION	f_chiral_restr	0.082	396
X-RAY DIFFRACTION	f_plane_restr	0.006	469

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 (%)
1.55-1.5816	0.2452	131	0.2513	2487	X-RAY DIFFRACTION	100
1.5816-1.616	0.2779	134	0.2292	2556	X-RAY DIFFRACTION	100
1.616-1.6536	0.2843	134	0.2218	2544	X-RAY DIFFRACTION	100
1.6536-1.695	0.263	134	0.2126	2550	X-RAY DIFFRACTION	100
1.695-1.7408	0.2621	135	0.2139	2563	X-RAY DIFFRACTION	100
1.7408-1.792	0.2409	135	0.2057	2554	X-RAY DIFFRACTION	100
1.792-1.8499	0.249	134	0.1973	2542	X-RAY DIFFRACTION	100
1.8499-1.916	0.2132	137	0.194	2600	X-RAY DIFFRACTION	100
1.916-1.9927	0.2462	134	0.1854	2540	X-RAY DIFFRACTION	100
1.9927-2.0834	0.1995	134	0.1814	2564	X-RAY DIFFRACTION	100
2.0834-2.1932	0.2118	137	0.1703	2590	X-RAY DIFFRACTION	100
2.1932-2.3306	0.217	135	0.1709	2571	X-RAY DIFFRACTION	100
2.3306-2.5105	0.2036	136	0.1693	2601	X-RAY DIFFRACTION	100
2.5105-2.7631	0.2327	138	0.1757	2593	X-RAY DIFFRACTION	100
2.7631-3.1628	0.2025	137	0.1736	2620	X-RAY DIFFRACTION	100
3.1628-3.9843	0.193	141	0.1586	2661	X-RAY DIFFRACTION	100
3.9843-41.3712	0.175	146	0.1716	2780	X-RAY DIFFRACTION	100

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	7.0037	2.1567	-3.121	5.8547	-2.1157	4.8374	-0.0111	-0.6523	-0.5001	0.9233	-0.4194	-0.252	0.3652	-0.2643	0.2649	0.4893	-0.0211	0.0024	0.3353	0.0297	0.2378	9.021	-13.8055	52.7712
2	4.0398	-0.0729	-1.2059	3.8157	1.1829	3.5563	-0.1986	0.2113	-0.0609	0.5022	-0.1178	0.133	0.1579	-0.3552	0.3159	0.3332	0.0507	-0.029	0.3641	-0.0149	0.179	5.4185	-8.3592	49.4056
3	1.4215	-0.7506	-1.3151	1.2601	1.426	1.8387	0.0399	-0.218	-0.0753	0.2423	-0.336	0.0914	-0.0282	-0.4862	0.1377	0.3488	0.0557	-0.1174	0.296	-0.0583	0.1699	5.1882	-5.5428	45.0829
4	0.9087	-2.3082	-1.8017	9.7879	6.1711	5.4306	-0.1114	0.038	-0.0986	0.6018	-0.0027	0.1178	0.2563	-0.2829	0.125	0.2426	0.0058	0.0044	0.1856	-0.0475	0.1427	6.4488	-14.6427	39.6484
5	1.1683	1.1799	-0.3985	7.8084	-4.0592	3.6609	-0.0336	0.0792	0.0054	-0.1091	-0.1675	-0.4789	0.3191	0.2256	0.2069	0.1342	0.0253	-0.0087	0.1801	0.0099	0.2042	12.0176	-11.1914	28.6576
6	1.0553	-0.2578	0.1659	2.2268	-1.6359	2.0178	-0.0714	-0.0951	0.3561	0.1111	-0.1127	-0.4562	-0.1398	0.1532	0.1478	0.1411	0.0076	-0.0233	0.156	-0.007	0.2167	10.331	0.7716	30.779
7	5.0998	-2.0541	1.4148	2.3882	-0.241	1.687	-0.2146	-0.3989	-0.2689	0.2279	0.2562	0.0276	-0.0711	-0.2183	-0.0267	0.2012	0.0327	-0.0067	0.1763	-0.0063	0.1388	3.4601	-6.5219	38.4047
8	6.6725	-1.4506	1.1557	7.9118	1.1368	4.8838	-0.3615	-0.2482	-0.2777	0.4036	0.091	0.479	0.4216	-0.3083	0.3015	0.2887	0.0142	0.0823	0.3595	0.0122	0.2713	-16.4655	-1.8616	33.6854
9	6.5128	-1.3248	-2.3595	2.7814	0.5025	3.1283	-0.0534	0.0003	0.2215	0.0219	-0.0161	-0.037	-0.2197	-0.0775	0.094	0.1165	0.0184	-0.0148	0.1197	0.0035	0.1126	-3.9999	6.8056	22.6832
10	1.7805	2.1114	-0.5977	3.7488	-0.2466	1.6994	0.0809	0.4467	0.3565	-0.0624	0.1322	0.597	-0.0473	-0.2496	-0.1784	0.2265	0.065	0.1207	0.3472	0.2088	0.6159	17.2424	-3.4257	16.6144
11	0.8568	0.597	0.1048	1.5793	-0.0706	1.8352	-0.2128	0.2648	-0.4423	-0.126	-0.0629	-0.0578	0.5868	-0.1058	-0.6161	0.4283	-0.0121	0.2028	0.2263	-0.0936	0.2713	0.0516	-15.1666	9.2382
12	0.4969	-0.3397	-0.0532	0.6602	-0.3646	0.3821	-0.0738	0.2377	-0.4211	-0.3666	-0.164	0.5004	0.5475	-0.4164	-0.3074	0.5346	-0.1759	0.0465	0.4409	-0.2512	0.4089	-13.0362	-17.5557	7.8371
13	7.8208	3.2712	-1.0536	6.0628	0.1529	3.2401	-0.1392	0.9824	0.1545	-0.8114	0.0152	0.295	0.1247	-0.3399	0.0078	0.4064	0.0155	0.0505	0.3492	0.0143	0.1576	-3.7139	-3.8526	3.4033
14	2.1457	-0.2434	-0.5733	1.9179	0.0825	1.7894	-0.0835	-0.1349	0.1428	0.1446	0.0272	-0.1161	-0.1008	-0.1257	0.0453	0.1125	0.0239	-0.0144	0.1427	-0.0121	0.1061	-1.7438	-0.6149	28.2851
15	4.9925	-0.2941	-1.635	0.9764	0.2131	1.7222	-0.1098	0.0751	-0.0629	-0.1281	0.0903	-0.0024	0.1251	-0.0296	0.0152	0.1407	-0.0018	0.0204	0.1252	0.0118	0.0746	-7.2455	-3.3551	18.5965
16	4.7873	1.8757	-2.7823	4.1158	-1.0227	2.4872	-0.1125	0.3784	0.3278	-0.2655	0.2017	0.1278	-0.107	-0.1838	-0.0961	0.1259	0.0161	-0.0023	0.152	0.0449	0.1177	-9.0597	7.48	15.4322
17	4.3481	1.7216	-1.2537	3.4983	-0.9972	3.0673	-0.1336	0.6959	0.1236	-0.4657	0.153	0.1542	0.0595	-0.3517	-0.0051	0.188	-0.0151	0.0132	0.2557	0.0051	0.1115	-9.2219	-1.4191	9.2956
18	1.6861	-0.9643	1.0776	3.0967	-2.0629	3.3634	-0.3132	-0.2232	-0.5478	0.2398	0.1716	0.3657	0.5386	-0.4509	-0.0576	0.5401	-0.0704	0.2523	0.2508	-0.0224	0.5533	-10.6939	-21.0472	23.0391

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	(CHAIN A AND RESID 2:13)
2	X-RAY DIFFRACTION	2	(CHAIN A AND RESID 14:29)
3	X-RAY DIFFRACTION	3	(CHAIN A AND RESID 30:46)
4	X-RAY DIFFRACTION	4	(CHAIN A AND RESID 47:53)
5	X-RAY DIFFRACTION	5	(CHAIN A AND RESID 54:70)
6	X-RAY DIFFRACTION	6	(CHAIN A AND RESID 71:85)
7	X-RAY DIFFRACTION	7	(CHAIN A AND RESID 86:105)
8	X-RAY DIFFRACTION	8	(CHAIN A AND RESID 106:117)
9	X-RAY DIFFRACTION	9	(CHAIN A AND RESID 118:139)
10	X-RAY DIFFRACTION	10	(CHAIN A AND RESID 140:145)
11	X-RAY DIFFRACTION	11	(CHAIN A AND RESID 146:168)
12	X-RAY DIFFRACTION	12	(CHAIN A AND RESID 169:186)
13	X-RAY DIFFRACTION	13	(CHAIN A AND RESID 187:193)
14	X-RAY DIFFRACTION	14	(CHAIN A AND RESID 194:223)
15	X-RAY DIFFRACTION	15	(CHAIN A AND RESID 224:240)
16	X-RAY DIFFRACTION	16	(CHAIN A AND RESID 241:256)
17	X-RAY DIFFRACTION	17	(CHAIN A AND RESID 257:271)
18	X-RAY DIFFRACTION	18	(CHAIN A AND RESID 272:299)

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