PDB-6bnc: Crystal structure of the intrinsic colistin resistance enzyme ICR...

ID or keywords:

Entry

Database: PDB / ID: 6bnc

Title

Crystal structure of the intrinsic colistin resistance enzyme ICR(Mc) from Moraxella catarrhalis, catalytic domain, Thr315Ala mutant di-zinc and PEG complex

Components

Phosphoethanolamine transferase

Keywords

TRANSFERASE /

antibiotic resistance / colistin / polymycin / phosphoethanolamine transferase / sulfatase fold / alpha/beta protein /

Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID

Function / homology

Function and homology information

transferase activity, transferring phosphorus-containing groups / sulfuric ester hydrolase activity /

plasma membrane
Similarity search - Function

Biological species

Moraxella sp. HMSC061H09 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 1.5 Å

Authors

Stogios, P.J. / Evdokimova, E. / Wawrzak, Z. / Savchenko, A. / Anderson, W.F. / Satchell, K.J. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)

Funding support

United States, 2items

Organization	Grant number	Country
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	HHSN272201200026C	United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	HHSN272201700060C	United States

Citation

Journal: ACS Chem. Biol. / Year: 2018
Title: Substrate Recognition by a Colistin Resistance Enzyme from Moraxella catarrhalis.
Authors: Stogios, P.J. / Cox, G. / Zubyk, H.L. / Evdokimova, E. / Wawrzak, Z. / Wright, G.D. / Savchenko, A.

History

Deposition	Nov 16, 2017	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jan 31, 2018	Provider: repository / Type: Initial release
Revision 1.1	Feb 14, 2018	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2	Apr 25, 2018	Group: Data collection / 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.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3	May 30, 2018	Group: Data collection / Database references / Category: citation Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.4	Dec 11, 2019	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	6bnc.cif.gz	304.2 KB	Display	PDBx/mmCIF format
PDB format	pdb6bnc.ent.gz	249.4 KB	Display	PDB format
PDBx/mmJSON format	6bnc.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/bn/6bnc ftp://data.pdbj.org/pub/pdb/validation_reports/bn/6bnc	HTTPS FTP

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Related structure data

Related structure data	6bndC 6bneC 6bnfC C: citing same article (ref.)
Similar structure data	3nfw-1 1l0d-1 1ke0-2 5ylf-d 4u0t-6 3gqz-1 5chj-1 1kvm-1 5cgs-d 4kg6-3 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
Other databases	TargetTrack: IDP-95742

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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: Phosphoethanolamine transferase

B: Phosphoethanolamine transferase

hetero molecules

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

1

A: Phosphoethanolamine transferase

hetero molecules

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

2

B: Phosphoethanolamine transferase

hetero molecules

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

Unit cell

Length a, b, c (Å)	74.051, 154.246, 66.392
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	18
Space group name H-M	P2₁2₁2

#1: Protein	Phosphoethanolamine transferase Mass: 37941.348 Da / Num. of mol.: 2 / Mutation: T315A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Moraxella sp. HMSC061H09 (bacteria) / Gene: HMPREF2573_04170 / Plasmid: pMCSG53 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)Gold / References: UniProt: A0A1E9VP98
#2: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-15P / POLYETHYLENE GLYCOL (N=34) / PEG 1500 / Polyethylene glycol Mass: 1529.829 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C₆₉H₁₄₀O₃₅ / Comment: precipitant*YM
#4: Chemical	ChemComp-CL / CHLORIDE ION / Chloride Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 1043 / 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: 2.5 Å³/Da / Density % sol: 50.77 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 0.1 M Tris pH 8, 28% (w/v) PEG 4k, 3 mM zinc chloride and 2 mM lipid A headgroup (Glycobiotech GmbH). Cryoprotectant paratone.

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.27815 Å
Detector	Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Dec 10, 2016
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.27815 Å / Relative weight: 1
Reflection	Resolution: 1.5→30 Å / Num. obs: 121223 / % possible obs: 99.9 % / Redundancy: 11.9 % / R_merge(I) obs: 0.088 / R_pim(I) all: 0.026 / Net I/σ(I): 30.68
Reflection shell	Resolution: 1.5→1.53 Å / Redundancy: 8.8 % / R_merge(I) obs: 0.595 / Mean I/σ(I) obs: 4.1 / Num. unique obs: 6059 / CC_1/2: 0.931 / R_pim(I) all: 0.203 / % possible all: 100

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Processing

Software

Name	Version	Classification
PHENIX	(dev_2733: ???)	refinement
HKL-3000		data reduction
HKL-3000		data scaling
PHENIX	phenix.phaser	phasing
PHENIX	phenix.autobuild	model building
Coot		model building

Refinement

Method to determine structure:

SAD / Resolution: 1.5→29.822 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 14.74

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.1527	10848	5.05 %	RANDOM
R_work	0.1316	-	-	-
obs	0.1327	214900	90.7 %	-

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.5→29.822 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5186	0	107	1043	6336

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.016	5535
X-RAY DIFFRACTION	f_angle_d	1.468	7535
X-RAY DIFFRACTION	f_dihedral_angle_d	17.45	2072
X-RAY DIFFRACTION	f_chiral_restr	0.125	834
X-RAY DIFFRACTION	f_plane_restr	0.011	986

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 (%)
1.4966-1.5136	0.2342	153	0.1978	3424	X-RAY DIFFRACTION	45
1.5136-1.5314	0.1783	265	0.175	4245	X-RAY DIFFRACTION	57
1.5314-1.5501	0.1743	262	0.1631	4690	X-RAY DIFFRACTION	63
1.5501-1.5697	0.1585	255	0.1477	5246	X-RAY DIFFRACTION	70
1.5697-1.5904	0.1735	278	0.1434	5536	X-RAY DIFFRACTION	74
1.5904-1.6122	0.1477	311	0.1402	5893	X-RAY DIFFRACTION	78
1.6122-1.6352	0.1643	294	0.1385	6152	X-RAY DIFFRACTION	82
1.6352-1.6596	0.1533	333	0.1431	6483	X-RAY DIFFRACTION	86
1.6596-1.6855	0.1534	389	0.1376	6669	X-RAY DIFFRACTION	89
1.6855-1.7132	0.1824	362	0.1427	6967	X-RAY DIFFRACTION	92
1.7132-1.7427	0.1512	343	0.1454	7129	X-RAY DIFFRACTION	95
1.7427-1.7744	0.1628	413	0.142	7269	X-RAY DIFFRACTION	97
1.7744-1.8085	0.1753	403	0.1377	7340	X-RAY DIFFRACTION	98
1.8085-1.8454	0.1523	382	0.1386	7466	X-RAY DIFFRACTION	99
1.8454-1.8855	0.1595	414	0.1301	7317	X-RAY DIFFRACTION	98
1.8855-1.9294	0.1649	415	0.1319	7429	X-RAY DIFFRACTION	99
1.9294-1.9776	0.1597	380	0.1269	7509	X-RAY DIFFRACTION	100
1.9776-2.0311	0.1543	431	0.1334	7470	X-RAY DIFFRACTION	100
2.0311-2.0908	0.1546	417	0.1316	7473	X-RAY DIFFRACTION	100
2.0908-2.1583	0.1569	358	0.1305	7546	X-RAY DIFFRACTION	100
2.1583-2.2354	0.1509	448	0.1237	7443	X-RAY DIFFRACTION	100
2.2354-2.3249	0.1642	348	0.1237	7546	X-RAY DIFFRACTION	100
2.3249-2.4307	0.1556	397	0.1228	7486	X-RAY DIFFRACTION	100
2.4307-2.5587	0.1547	410	0.1304	7506	X-RAY DIFFRACTION	100
2.5587-2.719	0.1666	419	0.1322	7409	X-RAY DIFFRACTION	100
2.719-2.9287	0.163	399	0.1299	7522	X-RAY DIFFRACTION	100
2.9287-3.2231	0.1404	407	0.1323	7416	X-RAY DIFFRACTION	99
3.2231-3.6888	0.1377	443	0.1194	7427	X-RAY DIFFRACTION	100
3.6888-4.6447	0.112	361	0.1024	7509	X-RAY DIFFRACTION	100
4.6447-29.8275	0.1642	358	0.163	7535	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	1.132	0.0561	-0.2504	0.5168	-0.0495	0.9785	-0.0274	-0.1566	-0.1276	0.0867	0.0203	-0.031	0.0007	0.0229	0.0088	0.0962	0.0165	-0.009	0.0766	0.023	0.0978	52.2944	53.2168	28.5507
2	0.9419	0.2543	-0.1936	1.0361	-0.4541	1.1102	-0.0238	-0.023	-0.0153	0.0321	0.0471	0.0067	-0.0075	-0.0804	-0.0289	0.062	0.014	0.0001	0.0591	0.0033	0.0712	43.6632	62.9564	22.5541
3	3.4435	-1.2871	-0.7499	3.8013	-0.8252	3.5247	0.017	0.6443	-0.2101	-0.4563	0.0067	-0.0536	0.1922	0.022	-0.0711	0.1276	-0.0104	0.0191	0.1617	-0.0446	0.1024	59.605	54.3152	4.0931
4	0.8897	-0.0216	-0.224	0.7562	0.1477	1.3079	-0.0414	-0.0567	-0.1355	0.0837	0.0224	-0.0655	0.12	0.0288	0.0097	0.072	0.0187	-0.0111	0.0628	0.0141	0.106	55.0011	51.6872	24.7286
5	8.5861	1.5722	-3.136	2.6841	1.6474	8.1405	0.1903	-0.5125	-0.0756	0.654	0.0965	0.3054	0.2236	-0.4298	-0.2699	0.2387	0.0271	0.0046	0.1911	0.1113	0.1943	49.5521	48.3259	41.3011
6	1.2922	0.0832	-0.1337	0.5404	-0.0371	1.0681	-0.0366	0.1346	-0.1641	-0.095	0.0436	-0.0341	0.0498	0.0213	-0.0008	0.1015	-0.023	0.0001	0.0762	-0.0251	0.0843	20.3281	53.8956	5.0882
7	0.7542	-0.0035	0.0012	0.6032	0.1525	0.7812	-0.0243	0.0098	0.026	-0.024	0.0407	-0.0234	-0.0568	0.0429	-0.0251	0.079	-0.0111	0.0001	0.0745	-0.0019	0.0821	26.7536	64.8989	13.1401
8	2.3965	0.3322	-0.5638	4.7282	2.8344	2.8491	0.0036	-0.7438	-0.2376	0.6225	-0.0442	-0.1893	0.2004	0.1282	0.0494	0.1279	-0.0121	0.0154	0.3085	0.0886	0.156	9.3178	55.001	30.992
9	1.0267	0.1226	-0.255	0.7575	-0.2247	1.3303	-0.0402	0.0732	-0.1139	-0.1084	0.0414	0.0322	0.1147	-0.0404	-0.0031	0.0721	-0.0223	-0.0109	0.0678	-0.0136	0.0805	16.3395	54.1174	8.4947
10	8.3036	-1.7491	-2.7218	5.83	2.7536	4.1449	0.0357	0.7991	-0.1152	-0.6395	0.2688	-0.5068	-0.1721	0.1356	-0.0819	0.2311	-0.0671	0.0419	0.2361	-0.1214	0.1832	21.0806	50.3726	-8.1039

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	(chain A and resid 244:325)
2	X-RAY DIFFRACTION	2	(chain A and resid 326:426)
3	X-RAY DIFFRACTION	3	(chain A and resid 427:457)
4	X-RAY DIFFRACTION	4	(chain A and resid 458:566)
5	X-RAY DIFFRACTION	5	(chain A and resid 567:578)
6	X-RAY DIFFRACTION	6	(chain B and resid 244:334)
7	X-RAY DIFFRACTION	7	(chain B and resid 335:439)
8	X-RAY DIFFRACTION	8	(chain B and resid 440:458)
9	X-RAY DIFFRACTION	9	(chain B and resid 459:566)
10	X-RAY DIFFRACTION	10	(chain B and resid 567:578)

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