PDB-5kk4: Crystal Structure of the Plant Defensin NsD7 bound to Phosphatidi...

ID or keywords:

Entry

Database: PDB / ID: 5kk4

Title

Crystal Structure of the Plant Defensin NsD7 bound to Phosphatidic Acid

Components

NsD7

Keywords

ANTIMICROBIAL PROTEIN / defensin / phospholipid / oligomer / phosphatidic acid

Function / homology

Function and homology information

phosphatidic acid binding / vacuole / defense response / killing of cells of another organism
Similarity search - Function

Biological species

Nicotiana suaveolens x Nicotiana tabacum (plant)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.7 Å

Authors

Kvansakul, M. / Hulett, M.D. / Lay, F.T.

Funding support

Australia, 1items

Citation

Journal: Proc.Natl.Acad.Sci.USA / Year: 2016
Title: Binding of phosphatidic acid by NsD7 mediates the formation of helical defensin-lipid oligomeric assemblies and membrane permeabilization.
Authors: Kvansakul, M. / Lay, F.T. / Adda, C.G. / Veneer, P.K. / Baxter, A.A. / Phan, T.K. / Poon, I.K. / Hulett, M.D.

History

Deposition	Jun 21, 2016	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Oct 5, 2016	Provider: repository / Type: Initial release
Revision 1.1	Oct 19, 2016	Group: Database references
Revision 1.2	Jan 1, 2020	Group: Author supporting evidence / Data collection ...Author supporting evidence / Data collection / Database references / Derived calculations Category: citation / diffrn_source ...citation / diffrn_source / pdbx_audit_support / pdbx_struct_oper_list Item: _citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site ..._citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site / _pdbx_audit_support.country / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3	Sep 27, 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

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5kk4.cif.gz	193.1 KB	Display	PDBx/mmCIF format
PDB format	pdb5kk4.ent.gz	162 KB	Display	PDB format
PDBx/mmJSON format	5kk4.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	5kk4_validation.pdf.gz	2.4 MB	Display	wwPDB validaton report
Full document	5kk4_full_validation.pdf.gz	2.4 MB	Display
Data in XML	5kk4_validation.xml.gz	20.2 KB	Display
Data in CIF	5kk4_validation.cif.gz	27.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/kk/5kk4 ftp://data.pdbj.org/pub/pdb/validation_reports/kk/5kk4	HTTPS FTP

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Related structure data

Related structure data	4ab0S S: Starting model for refinement
Similar structure data	4usn-2 2fmt-1 4usn-6 4usn-5 61 2fmt-2 2q9e-d 1xpp-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	#199 - Jul 2016 Monellin similarity (1) #38 - Feb 2003 Potassium Channels similarity (1)

Deposited unit

A: NsD7

B: NsD7

C: NsD7

D: NsD7

E: NsD7

F: NsD7

hetero molecules

36.7 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author

Unit cell

Length a, b, c (Å)	107.470, 62.327, 53.644
Angle α, β, γ (deg.)	90.00, 118.69, 90.00
Int Tables number	5
Space group name H-M	C121

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Protein/peptide , 1 types, 6 molecules ABCDEF

#1: Protein/peptide	NsD7 Mass: 5470.621 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Nicotiana suaveolens x Nicotiana tabacum (plant) Plasmid: pPIC9 / Production host: Komagataella pastoris (fungus) / References: UniProt: C0HK49*PLUS

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Non-polymers , 5 types, 297 molecules

#2: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: C₂H₆O₂
#3: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO₄
#4: Chemical	ChemComp-ACT / ACETATE ION Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₂H₃O₂
#5: Chemical	ChemComp-44E / (2R)-3-(phosphonooxy)propane-1,2-diyl dihexanoate Mass: 368.360 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C₁₅H₂₉O₈P / Comment: phospholipid*YM
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 266 / 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: 2.41 Å³/Da / Density % sol: 48.62 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.9 Details: 0.2 M ammonium sulfate, 25% PEG MME 2000, and 0.1 M sodium acetate pH 4.9

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
Detector	Type: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 3, 2014
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9537 Å / Relative weight: 1
Reflection	Resolution: 1.7→47.14 Å / Num. obs: 34010 / % possible obs: 99.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.7 % / CC_1/2: 0.998 / R_sym value: 0.067 / Net I/σ(I): 11.2
Reflection shell	Resolution: 1.7→1.73 Å / Redundancy: 3.8 % / R_merge(I) obs: 0.781 / Mean I/σ(I) obs: 1.5 / % possible all: 98

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Processing

Software

Name	Version	Classification
PHENIX	(1.10_2155: ???)	refinement
XDS		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 4AB0

4ab0

Resolution: 1.7→25.996 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.16 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2125	1736	5.11 %	Random selection
R_work	0.1834	-	-	-
obs	0.1849	33995	99.15 %	-

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.7→25.996 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2222	0	249	266	2737

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.009	2500
X-RAY DIFFRACTION	f_angle_d	1.347	3301
X-RAY DIFFRACTION	f_dihedral_angle_d	15.64	1677
X-RAY DIFFRACTION	f_chiral_restr	0.055	338
X-RAY DIFFRACTION	f_plane_restr	0.006	401

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 (%)
1.7-1.75	0.3095	140	0.2806	2664	X-RAY DIFFRACTION	99
1.75-1.8065	0.2763	135	0.2514	2658	X-RAY DIFFRACTION	99
1.8065-1.8711	0.2603	143	0.2328	2680	X-RAY DIFFRACTION	99
1.8711-1.946	0.2723	147	0.2195	2654	X-RAY DIFFRACTION	99
1.946-2.0345	0.2461	145	0.1968	2672	X-RAY DIFFRACTION	99
2.0345-2.1417	0.2192	141	0.1811	2713	X-RAY DIFFRACTION	99
2.1417-2.2758	0.2174	134	0.1657	2666	X-RAY DIFFRACTION	99
2.2758-2.4514	0.2005	156	0.1665	2693	X-RAY DIFFRACTION	100
2.4514-2.6979	0.233	153	0.1757	2710	X-RAY DIFFRACTION	100
2.6979-3.0877	0.1799	162	0.1777	2680	X-RAY DIFFRACTION	100
3.0877-3.8881	0.1779	156	0.171	2720	X-RAY DIFFRACTION	100
3.8881-25.9989	0.2118	124	0.1738	2749	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	3.9093	0.7947	-1.6433	7.3799	-4.9505	3.7211	-0.0356	-0.4206	0.3512	0.3334	-0.0842	-0.4797	-0.3571	0.2352	-0.0378	0.1719	0.0636	-0.0178	0.2109	-0.0786	0.2092	-14.204	-6.0921	-11.3914
2	3.5548	-0.8271	1.6016	1.6493	-1.0916	3.4759	0.2417	0.2664	-0.2991	-0.1475	-0.0572	0.0654	0.3909	-0.0082	-0.1357	0.1592	0.0366	-0.0554	0.1386	-0.0381	0.1626	-12.3312	-17.4654	-12.0087
3	1.4761	-0.1156	1.3258	1.1004	-1.1148	3.0908	0.0019	-0.0747	0.111	0.0604	-0.0838	-0.0015	-0.1051	-0.1055	0.0605	0.1655	0.0236	-0.0452	0.117	-0.0301	0.1395	-9.4811	-10.3183	-9.093
4	6.9092	4.9153	-6.2233	3.7356	-5.1838	8.1878	-0.1035	-0.0589	-0.1336	0.2379	-0.3667	-0.0107	0.0413	0.3824	-0.0297	0.1508	0.0318	-0.0045	0.1543	-0.0345	0.2224	-16.1472	-1.5555	-8.7043
5	3.5345	0.8963	0.9601	1.7894	-1.1387	5.3823	0.1424	0.1719	0.4871	0.0724	-0.0868	0.0238	-0.2774	0.1723	0.0138	0.2398	0.0165	0.0683	0.1231	-0.0083	0.1843	-11.2645	11.2519	-5.9303
6	8.4398	1.4076	4.2682	4.2305	4.5244	6.7613	-0.007	0.2339	1.2763	-0.3571	-0.3485	0.2371	-0.6469	-0.065	0.1593	0.2388	0.0811	0.0301	0.1637	0.0066	0.3566	-19.587	11.1485	-6.4239
7	3.9483	1.3524	0.9103	1.2935	-0.2393	3.5917	0.2536	-0.0117	0.1364	0.0816	-0.1491	0.2043	-0.0975	0.007	0.0237	0.155	0.0548	0.0172	0.1324	-0.0233	0.1559	-13.0957	4.9387	-4.6209
8	9.6236	4.0969	-0.3797	3.558	-2.0749	3.0011	-0.0173	0.2432	-0.551	0.0607	0.0332	-0.0151	-0.1732	-0.1231	-0.1069	0.1262	0.0896	0.0201	0.1712	-0.0383	0.2356	-18.5806	0.4538	-7.9931
9	8.334	-3.9532	-2.5698	8.7545	2.803	2.4221	-0.0915	-0.0837	0.5868	-0.0718	-0.1936	0.2764	-0.7073	0.4313	0.2849	0.1939	-0.0278	-0.0023	0.1447	-0.0223	0.2273	-2.9236	14.9725	19.6166
10	4.3455	-0.5022	-0.0503	3.1409	0.1838	4.7819	-0.0352	0.0543	-0.4694	0.2328	-0.049	0.0512	0.4256	0.1243	0.2751	0.1641	-0.0043	0.0765	0.098	0.0017	0.2108	-4.6002	1.8062	17.6689
11	4.1934	0.0482	0.8877	2.724	1.0896	4.6423	0.0743	-0.3603	0.0587	0.3025	-0.0479	-0.065	-0.0603	0.0929	-0.0209	0.1285	-0.0312	0.048	0.1454	-0.0113	0.1644	-6.0396	8.1597	21.0799
12	3.7655	0.0506	-0.9688	1.9515	0.014	3.9984	0.0052	-0.0431	-0.0435	0.026	-0.0762	0.18	-0.3392	0.4094	-0.1379	0.1306	-0.0718	0.0278	0.1561	-0.0178	0.1326	-3.0251	10.2477	14.3619
13	5.1956	-2.1966	1.2279	7.3081	-1.1585	4.6424	-0.3187	0.2573	-0.4193	0.2981	0.0379	-0.1131	0.2412	0.046	0.0423	0.1833	-0.0423	0	0.1771	0.0251	0.2066	0.8218	18.8308	19.6862
14	3.5442	-0.8733	-1.3884	2.447	0.0412	5.1229	0.0325	-0.0479	0.3647	0.0931	0.167	0.0313	-0.3466	-0.0241	-0.0414	0.194	-0.0293	-0.0142	0.1858	0.0459	0.1676	-0.3247	32.8436	14.6817
15	3.4312	3.7643	-0.8544	6.4707	-3.4316	2.8299	-0.1958	-0.0319	0.1677	0.5416	-0.2166	-0.5725	-0.7053	0.2143	0.0452	0.2603	-0.0781	-0.0984	0.1677	0.0296	0.2035	5.3562	31.5908	20.9189
16	3.4175	-0.1323	0.5932	2.4998	-1.6194	4.3427	0.0709	-0.1548	0.1978	0.3121	-0.133	-0.1113	-0.3161	0.0815	-0.0578	0.1819	-0.0664	-0.0311	0.162	0.0244	0.1246	3.7968	25.9427	21.5231
17	2.6425	-0.8917	1.0607	1.8467	-1.1658	5.2409	-0.0093	-0.0167	-0.1895	-0.0682	0.2271	-0.0414	0.5255	-0.5175	-0.225	0.1721	-0.0889	-0.0359	0.1836	0.034	0.1419	1.5874	23.9424	14.5006
18	5.8994	6.1842	-0.5137	9.4183	0.5893	0.4778	0.3482	-0.4007	0.8117	0.8164	0.2423	0.1216	-0.1348	-0.3683	-0.1794	0.2643	0.0731	0.0273	0.2599	0.0612	0.2676	17.5218	36.1749	-6.502
19	2.8445	-0.1619	0.5101	2.7115	0.7511	3.7646	-0.1874	-0.1393	-0.0671	0.2447	0.0805	0.0488	0.7569	0.255	0.032	0.2305	0.0504	-0.0144	0.158	0.0272	0.1471	10.8962	22.283	-5.5192
20	3.2892	0.3322	-0.1735	1.8868	0.5926	2.3501	0.134	0.0042	-0.4571	0.1639	-0.1183	-0.2231	0.2877	0.3674	0.0245	0.1919	0.1011	-0.0198	0.2353	0.0324	0.1672	15.847	26.4105	-3.3166
21	4.6558	5.6942	0.0614	6.8278	0.3939	1.408	-0.0696	0.0571	-0.0336	-0.3259	0.0385	-0.3257	0.4	0.0126	-0.0999	0.1508	0.1509	0.0053	0.2106	0.0448	0.2034	19.4841	33.161	-6.2052
22	1.1904	2.5681	3.0035	5.6833	6.6371	7.6816	0.1104	-0.3124	-0.4574	-0.4183	-0.1598	0.3104	-0.0789	0.1951	0.227	0.2369	0.0585	0.0103	0.2298	0.0292	0.3249	16.0469	39.2819	-10.9009
23	2.9833	0.875	-0.4237	1.8951	1.0926	2.8476	0.3911	-0.0067	0.1638	0.1744	-0.2077	-0.2513	-0.4172	-0.0399	-0.0199	0.2129	-0.0314	0.0118	0.201	0.0668	0.2542	13.1327	53.4636	-7.537
24	8.2776	-4.2673	-1.0677	2.4181	-0.2539	3.809	0.1494	0.6648	0.4098	-0.5356	-0.2811	-0.272	-0.246	0.2998	0.0417	0.3052	0.0024	0.0392	0.2399	0.1196	0.2722	15.1582	51.8638	-15.8984
25	3.615	-0.6763	-0.9122	2.4193	0.5322	4.1013	0.0229	0.0169	-0.2249	-0.2286	0.034	-0.0768	0.0386	0.2553	0.0785	0.1532	0.0246	-0.0088	0.1952	0.0565	0.1968	13.4856	45.0801	-10.9122

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 1 through 6 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 7 through 34 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 35 through 47 )
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 1 through 6 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 7 through 17 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 18 through 26 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 27 through 40 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 41 through 47 )
9	X-RAY DIFFRACTION	9	chain 'C' and (resid 1 through 6 )
10	X-RAY DIFFRACTION	10	chain 'C' and (resid 7 through 26 )
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 27 through 34 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 35 through 47 )
13	X-RAY DIFFRACTION	13	chain 'D' and (resid 1 through 6 )
14	X-RAY DIFFRACTION	14	chain 'D' and (resid 7 through 16 )
15	X-RAY DIFFRACTION	15	chain 'D' and (resid 17 through 26 )
16	X-RAY DIFFRACTION	16	chain 'D' and (resid 27 through 34 )
17	X-RAY DIFFRACTION	17	chain 'D' and (resid 35 through 47 )
18	X-RAY DIFFRACTION	18	chain 'E' and (resid 0 through 6 )
19	X-RAY DIFFRACTION	19	chain 'E' and (resid 7 through 16 )
20	X-RAY DIFFRACTION	20	chain 'E' and (resid 17 through 40 )
21	X-RAY DIFFRACTION	21	chain 'E' and (resid 41 through 47 )
22	X-RAY DIFFRACTION	22	chain 'F' and (resid 0 through 6 )
23	X-RAY DIFFRACTION	23	chain 'F' and (resid 7 through 16 )
24	X-RAY DIFFRACTION	24	chain 'F' and (resid 17 through 26 )
25	X-RAY DIFFRACTION	25	chain 'F' and (resid 27 through 47 )

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Non-polymers , 5 types, 297 molecules

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Experimental details

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Experiment

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Sample preparation

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Data collection

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Processing

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Yorodumi