PDB-5nuq: Structural basis for maintenance of bacterial outer membrane lipi...

ID or keywords:

Entry

Database: PDB / ID: 5nuq

Title

Structural basis for maintenance of bacterial outer membrane lipid asymmetry

Components

Outer membrane protein F
Probable phospholipid-binding lipoprotein mlaA

Keywords

MEMBRANE PROTEIN / Outer membrane / lipid asymmetry / lipoprotein / phospholipid translocation

Function / homology

Function and homology information

colicin transmembrane transporter activity / monoatomic ion channel complex / porin activity / pore complex / protein homotrimerization / monoatomic ion transmembrane transport / lipopolysaccharide binding / cell outer membrane / disordered domain specific binding / protein transport ...
Similarity search - Function

Biological species

Escherichia coli (E. coli)

Serratia marcescens (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 3.2 Å

Authors

Abellon-Ruiz, J. / Kaptan, S.S. / Basle, A. / Claudi, B. / Bumann, D. / Kleinekathofer, U. / van den Berg, B.

Funding support

United Kingdom, 1items

Citation

Journal: Nat Microbiol / Year: 2017
Title: Structural basis for maintenance of bacterial outer membrane lipid asymmetry.
Authors: Abellon-Ruiz, J. / Kaptan, S.S. / Basle, A. / Claudi, B. / Bumann, D. / Kleinekathofer, U. / van den Berg, B.

History

Deposition	May 1, 2017	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Oct 25, 2017	Provider: repository / Type: Initial release
Revision 1.1	Nov 1, 2017	Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2	Dec 6, 2017	Group: Database references / Category: citation Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3	Jan 17, 2024	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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PDBx/mmCIF format	5nuq.cif.gz	931.8 KB	Display	PDBx/mmCIF format
PDB format	pdb5nuq.ent.gz	782.1 KB	Display	PDB format
PDBx/mmJSON format	5nuq.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	5nuq_validation.pdf.gz	1.8 MB	Display	wwPDB validaton report
Full document	5nuq_full_validation.pdf.gz	1.9 MB	Display
Data in XML	5nuq_validation.xml.gz	84.8 KB	Display
Data in CIF	5nuq_validation.cif.gz	113.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/nu/5nuq ftp://data.pdbj.org/pub/pdb/validation_reports/nu/5nuq	HTTPS FTP

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Related structure data

Related structure data	5nuoC 5nupC 5nurC 2zfgS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	3cvr-2 5c3r-d 5c3s-d 3v98-d 7bw0-d 3044 4x6g-2 2b5l-2 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

Deposited unit

A: Outer membrane protein F

B: Outer membrane protein F

C: Outer membrane protein F

D: Outer membrane protein F

E: Outer membrane protein F

F: Outer membrane protein F

G: Probable phospholipid-binding lipoprotein mlaA

H: Probable phospholipid-binding lipoprotein mlaA

hetero molecules

278 kDa, 8 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Outer membrane protein F

C: Outer membrane protein F

E: Outer membrane protein F

H: Probable phospholipid-binding lipoprotein mlaA

hetero molecules

defined by author
139 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Outer membrane protein F

D: Outer membrane protein F

F: Outer membrane protein F

G: Probable phospholipid-binding lipoprotein mlaA

hetero molecules

defined by author
139 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	115.491, 163.039, 230.740
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Outer membrane protein F / Outer membrane protein 1A / Outer membrane protein B / Outer membrane protein IA / Porin OmpF Mass: 37114.250 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (strain K12) (bacteria) Strain: K12 / Gene: ompF, cmlB, coa, cry, tolF, b0929, JW0912 / Production host: Escherichia coli (E. coli) / References: UniProt: P02931
#2: Protein	Probable phospholipid-binding lipoprotein mlaA Mass: 26299.443 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Serratia marcescens (bacteria) / Gene: mlaA, ERS381432_02710 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0U8E5M0
#3: Chemical	ChemComp-C8E / (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE Mass: 306.438 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C₁₆H₃₄O₅ / Comment: C8E, detergent*YM

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 3.95 Å³/Da / Density % sol: 68.83 %
Crystal grow	Temperature: 295 K / Method: vapor diffusion, sitting drop Details: 0.32 M lithium chloride 0.1M Sodium citrate pH 5.5 and 14% PEG 400

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.97886 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 16, 2016
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97886 Å / Relative weight: 1
Reflection	Resolution: 3.2→94.242 Å / Num. obs: 72631 / % possible obs: 100 % / Redundancy: 7.6 % / CC_1/2: 0.985 / R_pim(I) all: 0.148 / Net I/σ(I): 4.5
Reflection shell	Resolution: 3.2→3.27 Å / Redundancy: 7.5 % / Mean I/σ(I) obs: 1.7 / Num. unique obs: 4398 / CC_1/2: 0.724 / R_pim(I) all: 0.494 / % possible all: 100

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Processing

Software

Name	Version	Classification
XDS		data reduction
xia2		data reduction
Aimless		data scaling
PHASER		phasing
PHENIX	(1.11.1_2575: ???)	refinement
Coot		model building

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 2ZFG

2zfg

Resolution: 3.2→94.242 Å / SU ML: 0.48 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.39

	R_factor	Num. reflection	% reflection
R_free	0.3065	5662	7.82 %
R_work	0.2383	-	-
obs	0.2436	72392	99.77 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 3.2→94.242 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	18952	0	100	0	19052

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	19472
X-RAY DIFFRACTION	f_angle_d	1.302	26317
X-RAY DIFFRACTION	f_dihedral_angle_d	7.055	11115
X-RAY DIFFRACTION	f_chiral_restr	0.063	2660
X-RAY DIFFRACTION	f_plane_restr	0.008	3531

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 (%)
3.2-3.2364	0.4043	214	0.3365	2132	X-RAY DIFFRACTION	100
3.2364-3.2744	0.3956	204	0.3274	2202	X-RAY DIFFRACTION	100
3.2744-3.3144	0.3289	180	0.3143	2199	X-RAY DIFFRACTION	100
3.3144-3.3563	0.4182	182	0.2835	2190	X-RAY DIFFRACTION	100
3.3563-3.4005	0.3569	194	0.2658	2226	X-RAY DIFFRACTION	100
3.4005-3.4471	0.2984	189	0.2621	2194	X-RAY DIFFRACTION	100
3.4471-3.4963	0.3295	196	0.2693	2200	X-RAY DIFFRACTION	100
3.4963-3.5485	0.3118	164	0.274	2217	X-RAY DIFFRACTION	100
3.5485-3.604	0.3427	193	0.2779	2189	X-RAY DIFFRACTION	100
3.604-3.6631	0.3286	179	0.2696	2190	X-RAY DIFFRACTION	100
3.6631-3.7262	0.3505	188	0.2442	2230	X-RAY DIFFRACTION	100
3.7262-3.794	0.3485	186	0.2464	2172	X-RAY DIFFRACTION	100
3.794-3.867	0.3513	184	0.2489	2236	X-RAY DIFFRACTION	100
3.867-3.9459	0.3168	184	0.2414	2180	X-RAY DIFFRACTION	100
3.9459-4.0317	0.2908	181	0.2291	2223	X-RAY DIFFRACTION	100
4.0317-4.1255	0.3336	198	0.2315	2213	X-RAY DIFFRACTION	100
4.1255-4.2287	0.3142	200	0.2237	2201	X-RAY DIFFRACTION	100
4.2287-4.343	0.3114	166	0.2116	2239	X-RAY DIFFRACTION	100
4.343-4.4708	0.2686	168	0.2163	2229	X-RAY DIFFRACTION	100
4.4708-4.6151	0.2653	188	0.2155	2255	X-RAY DIFFRACTION	100
4.6151-4.78	0.2611	187	0.2103	2203	X-RAY DIFFRACTION	100
4.78-4.9714	0.282	188	0.2099	2222	X-RAY DIFFRACTION	100
4.9714-5.1976	0.2731	210	0.2111	2214	X-RAY DIFFRACTION	100
5.1976-5.4716	0.2828	193	0.2014	2251	X-RAY DIFFRACTION	100
5.4716-5.8144	0.2648	188	0.2157	2238	X-RAY DIFFRACTION	100
5.8144-6.2633	0.2699	197	0.2114	2242	X-RAY DIFFRACTION	100
6.2633-6.8934	0.2579	182	0.2053	2289	X-RAY DIFFRACTION	100
6.8934-7.8904	0.292	177	0.2048	2263	X-RAY DIFFRACTION	100
7.8904-9.9394	0.2426	198	0.1946	2302	X-RAY DIFFRACTION	100
9.9394-94.283	0.2762	204	0.2498	2389	X-RAY DIFFRACTION	98

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	1.0223	-0.2026	-0.2681	1.214	-0.2688	1.3107	-0.0809	0.1363	-0.067	-0.0017	0.064	-0.1675	0.0221	0.0364	0.0207	0.4032	-0.0454	0.0513	0.2549	-0.0448	0.2294	-25.4579	-21.0446	4.6819
2	0.6365	-0.224	0.1147	0.7544	-0.4421	1.2128	-0.1364	-0.116	0.147	0.1699	0.0263	0.0732	0.0304	0.0375	0.0923	0.4716	-0.0268	-0.0131	0.2401	-0.0867	0.2874	-26.2191	-59.8195	30.2614
3	1.3366	-0.5877	0.1181	1.5799	0.3022	0.8642	-0.1397	-0.1618	0.1213	0.306	0.1015	-0.2128	0.1354	0.204	0.0309	0.5234	-0.0988	-0.0305	0.3184	-0.0576	0.2256	-20.0226	-5.6192	39.3918
4	1.2936	-0.1211	-0.4267	1.0284	-0.0562	0.2748	-0.0468	0.287	-0.0314	-0.2306	-0.051	0.0597	-0.0255	-0.0453	0.0988	0.4497	-0.0539	-0.0533	0.3606	-0.021	0.173	-20.6939	-75.5257	-4.3736
5	0.5271	-0.1055	0.2927	0.4025	0.0838	0.8377	-0.0951	0.0953	0.3466	0.1703	0.014	-0.2221	-0.6642	0.3095	0.0294	0.7771	-0.1457	0.1428	0.2755	0.0351	0.4303	-20.2687	16.74	8.0841
6	0.6627	-0.0815	-0.2823	0.9359	0.0376	0.4773	-0.2337	-0.0733	-0.3261	0.1508	-0.0093	0.0567	0.4707	-0.0254	0.132	0.7072	-0.0614	0.1316	0.2644	-0.0051	0.3501	-21.7535	-97.7178	26.8859
7	0.4271	0.2955	0.2512	0.5218	-0.2316	0.7772	-0.4277	-0.3787	-0.1609	0.2718	0.0503	0.0235	0.1528	-0.2745	0.1894	0.7657	0.0944	0.241	0.5584	0.055	0.3343	-42.0482	-85.6298	68.8215
8	0.2118	-0.4111	0.3542	1.1633	-0.0097	2.4892	-0.0548	0.2025	0.1066	-0.5467	-0.2621	-0.0519	-0.1922	0.0085	0.2772	0.4949	-0.0812	0.0281	0.4472	0.0758	0.3401	-41.0824	4.6151	-33.8766

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	(chain 'A' and resid 1 through 340)
2	X-RAY DIFFRACTION	2	(chain 'B' and resid 1 through 340)
3	X-RAY DIFFRACTION	3	(chain 'C' and resid 1 through 340)
4	X-RAY DIFFRACTION	4	(chain 'D' and resid 1 through 340)
5	X-RAY DIFFRACTION	5	(chain 'E' and resid 1 through 340)
6	X-RAY DIFFRACTION	6	(chain 'F' and resid 1 through 340)
7	X-RAY DIFFRACTION	7	(chain 'G' and resid 11 through 210)
8	X-RAY DIFFRACTION	8	(chain 'H' and resid 12 through 210)

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