PDB-6y0w: Fucosylated antimicrobial linear peptide cFucRH46D in complex wit...

ID or keywords:

Entry

Database: PDB / ID: 6y0w

Title

Fucosylated antimicrobial linear peptide cFucRH46D in complex with the fucose binding lectin LecB from Pseudomonas aeruginosa at 2.1 Angstrom resolution

Components

Fucose-binding lectin
cFucRH46D

Keywords

ANTIBIOTIC / Antimicrobial / Linear / Lectin

Function / homology

Function and homology information

single-species biofilm formation / carbohydrate binding / metal ion binding
Similarity search - Function

Biological species

Pseudomonas aeruginosa (bacteria)
synthetic construct (others)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 2.06 Å

Authors

Baeriswyl, S. / Stocker, A. / Reymond, J.-L.

Funding support

Switzerland, 1items

Citation

Journal: To Be Published
Title: Fucosylated antimicrobial linear peptide cFucRH46D in complex with the fucose binding lectin LecB from Pseudomonas aeruginosa at 2.1 Angstrom resolution
Authors: Baeriswyl, S. / Stocker, A. / Reymond, J.-L.

History

Deposition	Feb 10, 2020	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Feb 17, 2021	Provider: repository / Type: Initial release
Revision 1.1	Dec 7, 2022	Group: Database references / Category: database_2 Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2	Jan 31, 2024	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3	Nov 20, 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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PDBx/mmCIF format	6y0w.cif.gz	118.8 KB	Display	PDBx/mmCIF format
PDB format	pdb6y0w.ent.gz	91.1 KB	Display	PDB format
PDBx/mmJSON format	6y0w.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/y0/6y0w ftp://data.pdbj.org/pub/pdb/validation_reports/y0/6y0w	HTTPS FTP

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Related structure data

Related structure data	1oxcS S: Starting model for refinement
Similar structure data	5dcx-2 5dcx-1 6cen-d 6ijr-1 3x0t-d 5a9c-d 2rr3-d 2cqd-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

Deposited unit

A: Fucose-binding lectin

C: cFucRH46D

B: Fucose-binding lectin

D: cFucRH46D

hetero molecules

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

1

Idetical with deposited unit
defined by author&software
Evidence: mass spectrometry

Unit cell

Length a, b, c (Å)	68.999, 68.999, 271.453
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	178
Space group name H-M	P6₁22

Components on special symmetry positions

ID	Model	Components
1	1	A-437- HOH

#1: Protein	Fucose-binding lectin / Fucose-binding lectin II (PA-IIL) / Fucose-binding lectin PA-IIL Mass: 11865.905 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: Fucose binding lectin LecB PA-IIL from Pseudomonas aeruginosa Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) Gene: lecB, C0044_25260, CAZ10_21840, DT376_00595, DY979_15445, ECC04_10105, EFK27_13700, EGV95_09240, EGY23_15550, IPC669_23070, PA5486_01888, PAERUG_E15_London_28_01_14_00983, PAMH19_1713, RW109_RW109_02453 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: A0A069Q9V4, UniProt: Q9HYN5*PLUS
#2: Polypeptide(D)	cFucRH46D Mass: 1691.113 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Fucosylated linear antimicrobial peptide cFucRH46D / Source: (synth.) synthetic construct (others)
#3: Chemical	ChemComp-CA / CALCIUM ION Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#4: Sugar	ChemComp-ZDC / 3,7-anhydro-2,8-dideoxy-L-glycero-D-gluco-octonic acid Type: D-saccharide / Mass: 206.193 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Formula: C₈H₁₄O₆ / Feature type: SUBJECT OF INVESTIGATION
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 142 / 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: 3.47 Å³/Da / Density % sol: 64.54 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, sitting drop / Details: 25% w/v Polyethylene glycol 1,500

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

SLS

/ Beamline: X06DA / Wavelength: 1.03679 Å

Detector

Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Aug 19, 2016

Radiation

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

Radiation wavelength

Wavelength: 1.03679 Å / Relative weight: 1

Reflection

Resolution: 2.06→44.847 Å / Num. obs: 24853 / % possible obs: 99.9 % / Redundancy: 8.9 % / R_pim(I) all: 0.022 / R_rim(I) all: 0.067 / R_sym value: 0.063 / Net I/av σ(I): 10.6 / Net I/σ(I): 22

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. measured all	Num. unique obs	R_pim(I) all	R_rim(I) all	R_sym value	Net I/σ(I) obs	% possible all
2.06-2.17	8	0.927	0.8	27867	3493	0.349	0.993	0.927	2.4	99.2
2.17-2.3	8.8	0.639	1.2	29505	3366	0.228	0.679	0.639	3.7	100
2.3-2.46	9.3	0.383	2	29270	3133	0.132	0.405	0.383	5.9	100
2.46-2.66	9.4	0.273	2.8	27805	2954	0.093	0.289	0.273	8.2	100
2.66-2.91	8.7	0.145	5.3	23590	2724	0.052	0.154	0.145	13.7	100
2.91-3.26	9.3	0.08	9.5	23425	2506	0.027	0.085	0.08	23.8	100
3.26-3.76	9.5	0.043	16.6	21216	2234	0.015	0.045	0.043	44.9	100
3.76-4.61	9	0.03	22.2	17502	1940	0.011	0.032	0.03	58.4	100
4.61-6.51	8	0.024	25.1	12261	1534	0.009	0.026	0.024	65.3	100
6.51-44.847	8.3	0.018	29.9	8068	968	0.007	0.02	0.018	75.6	99.6

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Phasing

Phasing	Method: molecular replacement

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Processing

Software

Name	Version	Classification
PHENIX	v.1.11.1-2575	refinement
XDS		data reduction
SCALA	3.3.22	data scaling
PHASER		phasing
PDB_EXTRACT	3.25	data extraction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1OXC

1oxc

Resolution: 2.06→44.847 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.32 / Phase error: 24.95

	R_factor	Num. reflection	% reflection
R_free	0.2219	2221	4.98 %
R_work	0.1754	-	-
obs	0.1778	24837	99.71 %

Solvent computation

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

Displacement parameters

B_iso max: 143.18 Å² / B_iso mean: 54.0855 Å² / B_iso min: 30 Å²

Refinement step

Cycle: final / Resolution: 2.06→44.847 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1827	0	22	142	1991
B_iso mean	-	-	63.46	51.99	-
Num. residues	-	-	-	-	254

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	1896
X-RAY DIFFRACTION	f_angle_d	0.796	2601
X-RAY DIFFRACTION	f_chiral_restr	0.059	331
X-RAY DIFFRACTION	f_plane_restr	0.004	339
X-RAY DIFFRACTION	f_dihedral_angle_d	5.979	1024

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 (%)
2.06-2.1047	0.3496	134	0.3411	2593	97
2.1047-2.1537	0.355	143	0.2921	2652	100
2.1537-2.2075	0.2621	145	0.2644	2642	100
2.2075-2.2672	0.3247	137	0.2816	2593	99
2.2672-2.3339	0.2803	140	0.2274	2670	100
2.3339-2.4092	0.2707	137	0.2053	2646	100
2.4092-2.4953	0.2411	136	0.205	2667	100
2.4953-2.5952	0.2875	146	0.1963	2650	100
2.5952-2.7133	0.2593	131	0.2037	2647	100
2.7133-2.8564	0.2322	137	0.1869	2683	100
2.8564-3.0353	0.2562	139	0.1828	2640	100
3.0353-3.2696	0.2521	137	0.1922	2666	100
3.2696-3.5985	0.2259	136	0.1576	2655	100
3.5985-4.1189	0.1883	143	0.1513	2648	100
4.1189-5.1881	0.1517	136	0.1312	2662	100
5.1881-44.847	0.1859	144	0.147	2648	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	2.4693	1.9078	1.7981	4.0068	1.3549	1.4787	0.087	0.0366	-0.5314	-0.3592	0.1628	-0.6598	0.0379	0.3997	-0.2025	0.4408	0.0803	0.0709	0.2879	-0.0209	0.3932	23.0669	-38.2821	13.5103
2	3.3237	-1.6681	0.1423	7.1955	-0.6275	1.4243	0.1705	0.5095	0.1025	-0.557	-0.2947	-0.3868	-0.0502	-0.0021	0.095	0.6739	0.0125	0.1159	0.4167	0.0034	0.3465	21.0602	-28.3169	3.9943
3	5.0022	4.3605	-4.0975	3.8313	-3.6544	3.6121	-0.4057	0.1488	0.135	-0.2496	-0.3657	0.1635	-1.9774	-0.4931	0.7694	0.8644	0.097	0.0116	0.4762	0.0663	0.4885	11.9572	-15.7886	4.3104
4	1.5875	-0.7823	0.0738	4.1177	-1.3512	1.7311	0.1669	0.1287	-0.0915	-0.5028	-0.3268	-0.2713	0.1215	0.2027	0.1469	0.5132	0.084	0.1049	0.4063	-0.0498	0.3782	21.7534	-32.891	5.3347
5	3.7249	2.7553	-1.7259	3.1304	0.0198	2.5906	-0.3906	-0.3035	0.7096	-0.5748	0.4097	0.1457	-1.1119	0.4365	-0.023	0.8574	-0.1061	0.1198	0.3698	0.0512	0.4749	28.7704	-17.7713	7.5707
6	2.9541	1.6478	-1.4481	1.3352	-1.5759	2.6458	-0.0752	-0.1105	-0.0012	-0.1545	0.0272	-0.0283	0.2605	0.1109	0.0458	0.4868	0.081	0.0494	0.2824	-0.0215	0.3317	15.2329	-33.1565	16.3989
7	0.746	-0.0476	-0.4893	0.3685	-0.4906	1.2443	0.0906	0.1043	0.1122	-0.2513	-0.0996	0.0331	-0.0241	0.1375	-0.0222	0.4432	0.1014	0.0532	0.3327	-0.0231	0.3614	16.4639	-25.502	11.9216
8	3.0383	0.4024	0.4122	1.6998	-0.0892	4.2459	0.0345	0.1454	0.2289	-0.2403	0.0165	0.1205	-0.2155	-0.1888	0.0551	0.3686	0.1053	-0.0312	0.3267	0.0133	0.292	1.0685	-28.0312	12.7984
9	2.3856	0.2957	0.816	0.9963	-1.3492	2.4768	-0.1196	0.0364	0.0458	-0.0688	-0.1861	0.6117	-0.4618	-0.7031	0.1699	0.5426	0.114	-0.069	0.4421	-0.058	0.3333	-6.6634	-27.7405	10.5581
10	4.1454	-2.4684	-2.552	5.3496	5.415	5.4793	0.2371	0.6311	-0.4601	-0.6679	-0.1338	0.82	0.212	-0.6128	-0.2305	0.7445	0.1609	-0.1722	0.5664	-0.0066	0.4068	-6.2006	-26.5286	5.8053
11	5.4924	5.8847	3.0769	8.6646	2.4674	2.0237	0.3642	1.5165	0.0203	-0.5146	-0.1733	0.0371	0.2884	1.4603	-0.0729	0.849	0.0984	-0.0099	0.4918	-0.0529	0.3487	5.8625	-39.5706	-0.7821
12	0.642	0.6007	-0.6384	7.6207	6.3265	7.9259	-0.1598	0.0945	0.0968	-0.8578	0.1936	0.7599	-0.3666	-0.2552	-0.0137	0.6401	0.1085	-0.041	0.3945	0.0708	0.4124	2.1311	-24.1198	4.9351
13	3.1967	0.5381	-1.3394	9.2066	5.213	5.6201	-0.0245	-0.2089	0.3837	-0.9132	-0.2698	1.0579	-0.4373	-0.6865	0.4241	0.3861	0.1348	-0.1102	0.3986	-0.015	0.3885	-5.198	-25.5417	15.6335
14	1.3334	0.2283	0.0499	1.3669	-0.1405	1.8077	0.0023	-0.0359	0.0956	-0.0752	0.02	0.0582	-0.0087	-0.1509	-0.0587	0.3948	0.0805	-0.0034	0.2826	-0.0056	0.277	4.0198	-33.3271	14.0751

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 1 through 12 )	A	1 - 12
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 13 through 42 )	A	13 - 42
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 43 through 47 )	A	43 - 47
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 48 through 69 )	A	48 - 69
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 70 through 74 )	A	70 - 74
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 75 through 95 )	A	75 - 95
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 96 through 114 )	A	96 - 114
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 1 through 25 )	B	1 - 25
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 26 through 34 )	B	26 - 34
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 35 through 42 )	B	35 - 42
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 43 through 47 )	B	43 - 47
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 48 through 56 )	B	48 - 56
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 57 through 68 )	B	57 - 68
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 69 through 114 )	B	69 - 114

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