PDB-7waa: Crystal structure of MCR-1-S treated by AgNO3

ID or keywords:

Entry

Database: PDB / ID: 7waa

Title

Crystal structure of MCR-1-S treated by AgNO3

Components

Probable phosphatidylethanolamine transferase Mcr-1

Keywords

TRANSFERASE / MCR-1-S AgNO3 / ANTIBIOTIC

Function / homology

Function and homology information

phosphotransferase activity, phosphate group as acceptor / Transferases; Transferring phosphorus-containing groups / lipopolysaccharide core region biosynthetic process / response to antibiotic / plasma membrane
Similarity search - Function

Biological species

Escherichia coli (E. coli)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 1.58 Å

Authors

Zhang, Q. / Wang, M. / Sun, H.

Funding support

1items

Citation

Journal: Proc.Natl.Acad.Sci.USA / Year: 2022
Title: Re-sensitization of mcr carrying multidrug resistant bacteria to colistin by silver.
Authors: Zhang, Q. / Wang, R. / Wang, M. / Liu, C. / Koohi-Moghadam, M. / Wang, H. / Ho, P.L. / Li, H. / Sun, H.

History

Deposition	Dec 13, 2021	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Mar 16, 2022	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	7waa.cif.gz	263.3 KB	Display	PDBx/mmCIF format
PDB format	pdb7waa.ent.gz	221.2 KB	Display	PDB format
PDBx/mmJSON format	7waa.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	7waa_validation.pdf.gz	2.9 MB	Display	wwPDB validaton report
Full document	7waa_full_validation.pdf.gz	2.9 MB	Display
Data in XML	7waa_validation.xml.gz	24.4 KB	Display
Data in CIF	7waa_validation.cif.gz	34.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/wa/7waa ftp://data.pdbj.org/pub/pdb/validation_reports/wa/7waa	HTTPS FTP

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Related structure data

Similar structure data	6li5-d 6li6-d 6li4-d 6whf-d 3k1w-d 7biq-1 6zve-1 2npm-d 5gov-d 3g72-d 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	#50 - Feb 2004 Glycolytic Enzymes similarity (1)

Deposited unit

A: Probable phosphatidylethanolamine transferase Mcr-1

B: Probable phosphatidylethanolamine transferase Mcr-1

hetero molecules

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

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	47.200, 84.420, 81.760
Angle α, β, γ (deg.)	90.000, 98.670, 90.000
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Probable phosphatidylethanolamine transferase Mcr-1 / Polymyxin resistance protein MCR-1 Mass: 37231.473 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: mcr1, mcr-1, APZ14_31440 / Production host: Escherichia coli (E. coli) References: UniProt: A0A0R6L508, Transferases; Transferring phosphorus-containing groups
#2: Chemical	ChemComp-AG / SILVER ION Mass: 107.868 Da / Num. of mol.: 19 / Source method: obtained synthetically / Formula: Ag / Feature type: SUBJECT OF INVESTIGATION
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 96 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	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: 2.16 Å³/Da / Density % sol: 43.12 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 100mM Tris-HNO3, 32% PEG 3350, 25% Glycerol, pH 7.5, 1mM AgNO3, in the prevention of light

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

SSRF

/ Beamline: BL17U / Wavelength: 0.97915 Å

Detector

Type: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 19, 2018

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.97915 Å / Relative weight: 1

Reflection

Resolution: 1.58→42.21 Å / Num. obs: 85652 / % possible obs: 98.8 % / Redundancy: 6.8 % / CC_1/2: 0.997 / R_merge(I) obs: 0.063 / R_pim(I) all: 0.026 / R_rim(I) all: 0.068 / Net I/σ(I): 13.8 / Num. measured all: 580725 / Scaling rejects: 111

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. measured all	Num. unique obs	CC_1/2	R_pim(I) all	R_rim(I) all	Net I/σ(I) obs	% possible all
1.58-1.62	6.9	0.779	43940	6360	0.81	0.319	0.844	2.3	99.4
7.07-42.21	6.3	0.068	6294	1003	0.975	0.033	0.076	25.1	98.3

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Processing

Software

Name	Version	Classification
Aimless	0.6.2	data scaling
PHENIX	1.14_3219	refinement
PDB_EXTRACT	3.25	data extraction
HKL-2000		data reduction
PHENIX		phasing

Refinement

Method to determine structure:

SAD / Resolution: 1.58→42.21 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 24.47 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2125	4338	5.07 %
R_work	0.1931	81277	-
obs	0.1941	85615	98.74 %

Solvent computation

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

Displacement parameters

B_iso max: 78.23 Å² / B_iso mean: 37.5384 Å² / B_iso min: 20.79 Å²

Refinement step

Cycle: final / Resolution: 1.58→42.21 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5027	0	19	96	5142
B_iso mean	-	-	45.74	36.95	-
Num. residues	-	-	-	-	646

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / R_factor R_free error: 0

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	% reflection obs (%)
1.58-1.598	0.3381	134	0.2764	2746	100
1.598-1.6168	0.263	140	0.2632	2709	99
1.6168-1.6365	0.2412	129	0.2582	2715	99
1.6365-1.6572	0.27	128	0.2463	2719	99
1.6572-1.679	0.2388	128	0.2364	2731	99
1.679-1.702	0.2535	158	0.2393	2707	99
1.702-1.7263	0.2582	154	0.2292	2633	98
1.7263-1.7521	0.2811	151	0.2238	2690	98
1.7521-1.7795	0.2598	149	0.2205	2558	95
1.7795-1.8086	0.2485	146	0.2196	2690	98
1.8086-1.8398	0.249	144	0.2198	2721	100
1.8398-1.8733	0.2458	143	0.218	2746	100
1.8733-1.9093	0.2141	173	0.2078	2684	100
1.9093-1.9483	0.2515	152	0.2058	2723	100
1.9483-1.9906	0.2104	136	0.2099	2735	100
1.9906-2.037	0.1995	136	0.1995	2743	100
2.037-2.0879	0.2521	142	0.2108	2714	99
2.0879-2.1443	0.2364	128	0.211	2798	100
2.1443-2.2074	0.2251	144	0.2113	2669	99
2.2074-2.2787	0.2044	154	0.2	2712	99
2.2787-2.3601	0.1961	131	0.195	2748	99
2.3601-2.4546	0.2338	141	0.2143	2637	97
2.4546-2.5663	0.2404	141	0.2115	2608	95
2.5663-2.7016	0.2649	130	0.2197	2747	100
2.7016-2.8708	0.2439	149	0.2145	2756	100
2.8708-3.0924	0.2008	169	0.2	2709	100
3.0924-3.4035	0.2002	143	0.1961	2766	99
3.4035-3.8957	0.2232	156	0.1721	2720	99
3.8957-4.907	0.165	136	0.1437	2663	96
4.907-10	0.1845	173	0.1717	2780	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	2.4101	-0.308	0.4351	2.9275	-1.4898	1.9241	0.0712	0.0184	0.3403	-0.2024	0.0785	0.3891	-0.2033	-0.1533	-0.1359	0.3323	0.0016	-0.0172	0.2088	-0.0183	0.3266	-4.421	14.2934	3.0904
2	1.5565	-0.5506	0.3195	2.3663	0.668	1.8873	0.0184	0.1539	-0.0794	-0.0991	0.0278	-0.002	0.1297	0.1577	-0.0437	0.2811	-0.0075	-0.0034	0.2542	-0.0308	0.2537	9.3049	-6.2519	3.8382
3	5.944	-1.7498	-1.0219	3.1097	0.5081	2.629	0.0198	0.2502	0.6112	-0.3081	0.0671	-0.4812	-0.3824	0.4159	-0.0885	0.4331	-0.1044	-0.0109	0.3042	0.0589	0.3947	10.8116	16.7232	0.6493
4	1.5925	-0.553	0.2976	2.407	0.0378	2.0737	-0.1522	-0.1711	0.1926	0.1712	0.094	-0.1653	-0.2622	0.1753	0.0411	0.2919	-0.015	-0.0164	0.2594	-0.0288	0.2847	7.3109	10.8643	17.0767
5	5.6475	-2.7225	1.0482	2.8868	-0.8168	1.7418	-0.334	-0.6852	0.2032	0.3621	0.304	-0.0173	-0.0124	-0.2164	-0.0079	0.3044	-0.0004	0.0198	0.329	-0.0191	0.2489	3.926	1.207	23.0114
6	3.5581	-2.3562	1.4637	3.4412	-0.722	2.312	-0.0885	-0.119	0.0791	0.1741	0.1509	-0.0347	0.101	0.009	-0.0935	0.2724	-0.0258	-0.0034	0.2169	-0.0089	0.2404	8.6621	-1.7057	16.0916
7	3.3707	0.7497	-0.8101	3.3882	-0.2172	3.8705	0.0287	-0.372	-0.451	0.2892	0.289	-0.4096	0.4382	0.7699	-0.1932	0.4666	0.1527	-0.075	0.43	-0.0351	0.4648	22.7222	-16.1945	16.5369
8	3.0721	-0.4454	-0.0736	1.942	-0.0122	2.358	-0.0133	0.1886	-0.0575	-0.0295	0.0845	-0.0156	0.1839	0.1443	-0.0738	0.2623	-0.0299	-0.0369	0.1883	-0.026	0.226	8.6209	-4.9813	7.3101
9	2.8194	-1.3977	-0.8881	3.2923	0.8793	2.0004	0.1523	0.5253	0.0947	-0.6361	-0.1738	0.2785	-0.2022	-0.0569	0.0371	0.3745	-0.0022	-0.0684	0.3044	0.049	0.2635	0.4663	5.9238	-5.2986
10	1.7449	-0.0117	-0.1087	1.5722	0.1885	0.7473	0.121	-0.4486	-0.4035	0.3416	-0.2485	0.4034	0.3516	-0.5851	0.0933	0.4171	-0.2009	0.042	0.6003	-0.0458	0.4305	-8.9927	14.7105	48.7306
11	1.3639	1.1197	-0.0384	1.8375	0.1685	2.3754	0.0495	-0.0739	0.1309	-0.1258	-0.0773	0.1075	-0.0448	0.04	0.0184	0.3075	0.0238	0.0088	0.308	-0.069	0.2979	5.7482	24.5461	30.8136
12	3.0052	0.0263	-1.013	2.2063	0.0588	2.2994	-0.033	-0.2248	0.248	-0.1359	-0.2925	0.4628	-0.1541	-0.6906	0.3016	0.2803	0.0082	-0.0125	0.5605	-0.2319	0.4821	-15.9089	25.3936	39.9219
13	3.2949	1.2846	0.0819	1.5578	0.5252	0.7631	0.1944	-0.656	0.5026	0.3468	-0.3806	0.3517	-0.1445	-0.4692	0.0932	0.3111	-0.0408	0.04	0.5274	-0.1767	0.3355	1.6848	32.6878	49.7075
14	3.3151	1.9022	-0.2403	3.6711	-0.723	3.2636	0.1969	-0.208	0.2785	0.3115	-0.1115	0.1329	-0.17	-0.1468	-0.0932	0.2679	-0.0143	0.0002	0.3094	-0.1076	0.3161	6.805	31.4266	42.353
15	6.2276	1.6494	1.4915	2.813	1.0555	4.4006	-0.227	0.6473	0.9942	-0.8632	-0.0142	0.3011	-0.7628	0.5206	0.2408	0.5244	-0.1635	0.0074	0.5095	0.0554	0.4689	16.2825	41.911	26.7603
16	3.5334	1.5324	0.7334	2.1083	0.6712	1.8125	0.0505	-0.0178	0.1326	-0.1024	-0.114	0.021	-0.0835	0.0181	0.0718	0.2321	0.0277	0.0351	0.2564	-0.0783	0.2601	5.9914	26.2562	34.3468
17	1.9991	-0.3628	0.1006	1.6847	-0.34	3.4469	0.1503	-0.0698	-0.2812	0.1005	-0.2523	0.3733	0.388	-0.4982	0.1294	0.3421	-0.0702	0.0117	0.3747	-0.1057	0.4357	-6.5367	13.0197	36.3768

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 3 through 29 )	A	3 - 29
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 30 through 77 )	A	30 - 77
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 78 through 102 )	A	78 - 102
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 103 through 140 )	A	103 - 140
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 141 through 164 )	A	141 - 164
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 165 through 191 )	A	165 - 191
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 192 through 207 )	A	192 - 207
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 208 through 286 )	A	208 - 286
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 287 through 325 )	A	287 - 325
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 3 through 29 )	B	3 - 29
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 30 through 76 )	B	30 - 76
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 77 through 102 )	B	77 - 102
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 103 through 163 )	B	103 - 163
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 164 through 191 )	B	164 - 191
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 192 through 207 )	B	192 - 207
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 208 through 286 )	B	208 - 286
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 287 through 325 )	B	287 - 325

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