PDB-6li4: Crystal structure of MCR-1-S

ID or keywords:

Entry

Database: PDB / ID: 6li4

Title

Crystal structure of MCR-1-S

Components

Probable phosphatidylethanolamine transferase Mcr-1

Keywords

TRANSFERASE / MCR-1 Zn(II) / 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 /

MOLECULAR REPLACEMENT / Resolution: 1.78 Å

Authors

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

Funding support

Hong Kong, 1items

Citation

Journal: Nat Commun / Year: 2020
Title: Resensitizing carbapenem- and colistin-resistant bacteria to antibiotics using auranofin.
Authors: Sun, H. / Zhang, Q. / Wang, R. / Wang, H. / Wong, Y.T. / Wang, M. / Hao, Q. / Yan, A. / Kao, R.Y. / Ho, P.L. / Li, H.

History

Deposition	Dec 10, 2019	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Sep 16, 2020	Provider: repository / Type: Initial release
Revision 1.1	Oct 28, 2020	Group: Database references / Category: citation / citation_author Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2	Nov 22, 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
Revision 1.3	Oct 30, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	6li4.cif.gz	302.6 KB	Display	PDBx/mmCIF format
PDB format	pdb6li4.ent.gz	216 KB	Display	PDB format
PDBx/mmJSON format	6li4.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	6li4_validation.pdf.gz	1.7 MB	Display	wwPDB validaton report
Full document	6li4_full_validation.pdf.gz	1.7 MB	Display
Data in XML	6li4_validation.xml.gz	27.2 KB	Display
Data in CIF	6li4_validation.cif.gz	39 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/li/6li4 ftp://data.pdbj.org/pub/pdb/validation_reports/li/6li4	HTTPS FTP

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Related structure data

Related structure data	6lheC 6li5C 6li6C 5govS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	6li6-2 6li5-1 7cgd-4 2d7u-d 7cgd-3 5lrn-1 4fiz-d 5mx9-d 3bo5-d 3itd-d Search similar-shape structures by Omokage search (details) 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	#50 - Feb 2004 Glycolytic Enzymes similarity (1)

Deposited unit

A: Probable phosphatidylethanolamine transferase Mcr-1

B: Probable phosphatidylethanolamine transferase Mcr-1

hetero molecules

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

1

A: Probable phosphatidylethanolamine transferase Mcr-1

hetero molecules

defined by author
Evidence: gel filtration
37.3 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Probable phosphatidylethanolamine transferase Mcr-1

hetero molecules

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

Unit cell

Length a, b, c (Å)	46.970, 84.180, 81.400
Angle α, β, γ (deg.)	90.000, 98.760, 90.000
Int Tables number	4
Space group name H-M	P12₁1
Space group name Hall	P2yb

#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 BL21(DE3) (bacteria) References: UniProt: A0A0R6L508, Transferases; Transferring phosphorus-containing groups
#2: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 303 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y
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: 2.14 Å³/Da / Density % sol: 42.41 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 100mM KSCN, 32% PEG 3350, 100mM Tris-HNO3, pH 8.0

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Data collection

Diffraction

Mean temperature: 100 K / Ambient temp details: Nitrogen flow / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

SSRF

/ Beamline: BL17U1 / Wavelength: 0.97917 Å

Detector

Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 6, 2018 / Details: Null

Radiation

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

Radiation wavelength

Wavelength: 0.97917 Å / Relative weight: 1

Reflection

Resolution: 1.78→42.09 Å / Num. obs: 59043 / % possible obs: 98.5 % / Redundancy: 6.6 % / CC_1/2: 0.995 / R_merge(I) obs: 0.109 / R_pim(I) all: 0.046 / R_rim(I) all: 0.119 / Net I/σ(I): 8.7 / Num. measured all: 389264 / Scaling rejects: 100

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
1.78-1.83	6.9	0.761	29853	4319	0.917	0.31	0.823	1.8	97.4
7.96-42.09	6.1	0.067	4207	689	0.992	0.029	0.073	18	97.8

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Processing

Software

Name	Version	Classification
PHENIX	v1.15	refinement
XDS	Build 20180808	data reduction
Aimless	0.7.2	data scaling
PDB_EXTRACT	3.25	data extraction
PHASER	2.8.3	phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 5GOV

5gov

Resolution: 1.78→37.29 Å / SU ML: 0.2307 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 31.4286
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.2304	2852	4.86 %
R_work	0.1914	55884	-
obs	0.1933	58736	97.89 %

Solvent computation

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

Displacement parameters

B_iso mean: 39.03 Å²

Refinement step

Cycle: LAST / Resolution: 1.78→37.29 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5005	0	2	303	5310

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0064	5119
X-RAY DIFFRACTION	f_angle_d	0.8307	6975
X-RAY DIFFRACTION	f_chiral_restr	0.0521	780
X-RAY DIFFRACTION	f_plane_restr	0.0051	916
X-RAY DIFFRACTION	f_dihedral_angle_d	18.5833	1819

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 (%)
1.78-1.81	0.3402	126	0.3031	2774	X-RAY DIFFRACTION	96.25
1.81-1.84	0.3415	149	0.2876	2777	X-RAY DIFFRACTION	98.95
1.84-1.88	0.3252	130	0.269	2860	X-RAY DIFFRACTION	99.14
1.88-1.92	0.3417	148	0.251	2757	X-RAY DIFFRACTION	98.54
1.92-1.96	0.3024	141	0.2484	2811	X-RAY DIFFRACTION	98.01
1.96-2	0.3058	134	0.2432	2784	X-RAY DIFFRACTION	98.45
2-2.05	0.321	144	0.2472	2828	X-RAY DIFFRACTION	98.61
2.05-2.11	0.2962	132	0.2355	2787	X-RAY DIFFRACTION	98.65
2.11-2.17	0.3302	168	0.2351	2780	X-RAY DIFFRACTION	98.17
2.17-2.24	0.2515	143	0.2231	2833	X-RAY DIFFRACTION	98.61
2.24-2.32	0.2899	146	0.2183	2756	X-RAY DIFFRACTION	97.48
2.32-2.42	0.2623	143	0.2179	2744	X-RAY DIFFRACTION	96.52
2.42-2.53	0.2507	136	0.2237	2628	X-RAY DIFFRACTION	92.78
2.53-2.66	0.2303	142	0.2166	2796	X-RAY DIFFRACTION	97.64
2.66-2.83	0.2834	151	0.2113	2822	X-RAY DIFFRACTION	98.71
2.83-3.04	0.2345	144	0.1963	2805	X-RAY DIFFRACTION	98.66
3.04-3.35	0.1876	152	0.181	2852	X-RAY DIFFRACTION	98.95
3.35-3.83	0.2255	148	0.1685	2800	X-RAY DIFFRACTION	98.17
3.83-4.83	0.1742	131	0.1414	2800	X-RAY DIFFRACTION	96.83
4.83-37.29	0.1669	144	0.1595	2890	X-RAY DIFFRACTION	98.73

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	0.737987631237	-0.699229404463	0.138166267797	1.16263860966	0.306212100019	1.41239950011	-0.0283774811292	0.105813425369	0.0293842542477	-0.202637940666	0.0305754959782	0.14392465942	-0.0987950376564	0.0377782716715	-0.0173880285742	0.270405539819	-0.0397988051427	-0.0476413372203	0.245870012759	0.00319123725172	0.248367750377	4.80130564756	1.44070194917	3.47095731982
2	1.05430621003	-0.360266156033	0.228572039949	1.16392178979	0.309333542459	1.87891125156	-0.120068651774	0.0457735950776	0.242779287862	-0.110772250027	0.0845459061989	-0.0715959484642	-0.498408147969	0.184988431092	0.0605600679974	0.34763634709	-0.0495349985808	-0.0398431609657	0.241555837256	-0.000975298493221	0.300895915042	8.56403541213	13.2043922344	10.251930335
3	2.93574260167	-1.66004702754	0.639698506671	1.96343384881	-0.664894011934	1.15209026566	-0.197642965867	-0.204664859675	0.35522912449	0.159882251477	0.195908667331	-0.0290200990453	0.0295580562838	-0.305029969154	-0.00673646137683	0.257578692068	0.0108096882086	-0.0115823233032	0.351156152632	-0.0125508252157	0.324722849436	3.91597123202	1.29151000034	22.9535629796
4	1.25799511656	-0.655661752437	0.835109616823	1.81297595736	-0.327805391902	1.49803532656	-0.119391936249	0.0144406867702	0.0231204487686	0.0695767240401	0.113079938755	0.0300636982661	-0.0414916934731	-0.0650179498059	0.0274851059888	0.225490750676	-0.0172279713935	0.00559694068547	0.257655923124	-0.0111203987912	0.200376607379	8.71312713409	-1.05249137731	15.6381694865
5	2.980191153	0.383509175192	-1.1005564255	2.28202222144	-0.354125718157	2.67474150579	-0.263906036994	-0.137880261334	-0.0266108273123	0.453596040729	0.381824825657	-0.424095103723	0.546553872205	0.504353787353	-0.0198701530522	0.474042022636	0.10849899876	-0.0906242716872	0.417391946937	-0.0375593016639	0.370686117464	22.9212096547	-15.9653192283	16.4839719064
6	0.706249250376	-0.185033622707	0.531745562867	1.15860319133	-0.0712407523528	1.60016653969	-0.0579183641028	-0.0126931790994	-0.0352523134218	-0.0528028168605	0.0714133199391	0.0871136137381	0.166707445642	-0.0224624081786	-0.0255505498154	0.25985076806	-0.032099540414	-0.0351852789491	0.262329341095	-0.0064871439385	0.260636858639	8.99299939672	-5.74276602353	9.7799608074
7	5.16863542814	0.488967923059	-0.577060658935	1.75412599188	-0.0990739220481	1.70981635185	-0.19471500788	0.289748194724	0.219148702608	-0.208062233459	0.116128081499	0.106698562024	0.0757473160683	-0.0904984940127	0.126519233562	0.285004779334	-0.0527549184628	-0.0442468406188	0.296688556074	-0.00349896886458	0.216258365705	7.83921150373	-2.87939751552	0.592705883114
8	1.34040355988	-0.694455984712	-0.262893545969	1.36731875505	0.427499874471	0.90818019283	-0.037338162463	0.192466007845	0.00298866318838	-0.243781729327	0.0177801310863	0.329467039944	-0.289206717591	-0.168687645697	-0.000453635218527	0.444976510631	-0.00807545103306	-0.11043723023	0.28566868288	0.0191348651041	0.292964031521	0.392253379711	5.51809368279	-5.27243424382
9	1.36827802786	0.0231664228725	-0.401655220884	0.317803154663	0.364288221426	0.528324061652	0.19928660372	-0.471193714818	-0.403873565115	0.187736166243	-0.308128279383	0.203165612208	0.220522684811	-0.524652302986	0.026090713072	0.344485654946	-0.204781526476	-0.00594711036915	0.651414243981	0.0502052841356	0.357715077151	-10.5060085047	15.9942184993	47.9344899221
10	1.11351641792	0.34944619897	0.272567400359	0.804898194288	-0.109354900438	1.07461167339	0.0878774251193	-0.11962360105	-0.0767304324671	-0.104833936063	0.00908947478215	0.0596764000231	0.079223489652	-0.13856396842	-0.0730396080409	0.232185738936	0.0116858337113	-0.0113234448086	0.329224484322	-0.0410485624727	0.232567494463	5.58042439981	24.6051115925	30.411914827
11	1.74464631149	-0.334870974295	0.0288332635795	1.45138100809	-0.0864907093183	1.45808099912	0.165493211862	-0.219496935687	0.157418464229	-0.0122333862729	-0.039155808969	0.280700771291	-0.146645391497	-0.705051005757	-0.055967704616	0.262822214618	-0.0116822236086	0.00884402126402	0.684621127319	-0.0390222931493	0.400591438343	-15.8042202276	25.5610739623	39.5953067861
12	1.31417932574	0.618156558	0.334294720539	0.707198353389	0.1793654017	0.972736242755	0.14058603435	-0.489356683331	0.164534070918	0.195795074942	-0.178404470251	0.163565166596	-0.0714755878544	-0.442451916178	0.0272798883522	0.282551837559	-0.0309848499225	0.0294184534288	0.529089807839	-0.0637180465057	0.273671742495	1.58368256733	32.7392996287	49.1509840309
13	1.66992243339	1.20580845169	-0.600433988684	2.23862153243	-1.14715314215	2.13378034052	0.172134690181	-0.265382686014	-0.0949985488676	0.382086024948	-0.0131024691837	0.0461480630062	-0.0728354974642	-0.37501555498	-0.0939043050186	0.206546161426	-0.0413983442098	-0.00950164301811	0.362781575894	-0.00680456910786	0.233644810074	1.28579997008	27.3445304994	45.1086451033
14	1.83082326665	0.178543172953	-0.609543787066	1.37559483176	0.441547873775	1.77562954442	-0.031935542555	0.0956679595484	0.379592771238	-0.388532397276	0.0558726853288	-0.0828135077414	-0.39235581507	0.289503654583	0.0356399167058	0.306821211416	-0.0447447603949	0.0200731441073	0.329607774602	0.0125564195827	0.307978251431	15.6782573729	40.2726355623	31.1807957194
15	1.28308868892	0.481765224138	0.394890703381	0.809718895908	0.288395754962	1.25349735689	0.128044452619	-0.0183054283727	-0.10341039514	0.0301589545819	-0.0545607183537	0.114231106033	0.106238456878	-0.0801797779495	-0.0425433807703	0.22387080589	-0.000330791248946	0.00400450920281	0.333611284034	-0.00241221921572	0.242874917683	3.85321150415	23.9077026034	33.8238654526
16	2.89806027432	0.577605667878	-0.112967815287	0.157677274871	-0.266844607674	1.60684024794	0.0103526283481	-0.147301599982	-0.453033448092	0.0409771952159	-0.140742224262	0.384510112297	0.514431969506	-0.70048205993	-0.0333861625557	0.41849798403	-0.135355604433	-0.016119288913	0.501814270866	-0.0102697680433	0.492303013072	-9.80428212491	11.7906197559	37.7178673026

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 217 through 293 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 294 through 356 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 357 through 380 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 381 through 407 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 408 through 423 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 424 through 481 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 482 through 502 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 503 through 541 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 216 through 245 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 246 through 292 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 293 through 318 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 319 through 379 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 380 through 398 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 399 through 423 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 424 through 525 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 526 through 541 )

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