PDB-4ab0: X-ray crystal structure of Nicotiana alata defensin NaD1

ID or keywords:

Entry

Database: PDB / ID: 4ab0

Title

X-ray crystal structure of Nicotiana alata defensin NaD1

Components

FLOWER-SPECIFIC DEFENSIN

Keywords

ANTIMICROBIAL PROTEIN / INNATE IMMUNITY

Function / homology

Function and homology information

vacuole / defense response to fungus / killing of cells of another organism / extracellular region
Similarity search - Function

Biological species

NICOTIANA ALATA (Persian tobacco)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.636 Å

Authors

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

Citation

Journal: J.Biol.Chem. / Year: 2012
Title: Dimerization of Plant Defensin Nad1 Enhances its Antifungal Activity.
Authors: Lay, F.T. / Mills, G.D. / Poon, I.K. / Cowieson, N.P. / Kirby, N. / Baxter, A.A. / Van Der Weerden, N.L. / Dogovski, C. / Perugini, M.A. / Anderson, M.A. / Kvansakul, M. / Hulett, M.D.

History

Deposition	Dec 6, 2011	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Apr 25, 2012	Provider: repository / Type: Initial release
Revision 1.1	Jun 20, 2012	Group: Other
Revision 1.2	Nov 13, 2024	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	4ab0.cif.gz	53.5 KB	Display	PDBx/mmCIF format
PDB format	pdb4ab0.ent.gz	41.1 KB	Display	PDB format
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Validation report

Summary document	4ab0_validation.pdf.gz	425.5 KB	Display	wwPDB validaton report
Full document	4ab0_full_validation.pdf.gz	427.1 KB	Display
Data in XML	4ab0_validation.xml.gz	7.6 KB	Display
Data in CIF	4ab0_validation.cif.gz	9.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ab/4ab0 ftp://data.pdbj.org/pub/pdb/validation_reports/ab/4ab0	HTTPS FTP

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Related structure data

Related structure data	4aazC C: citing same article (ref.)
Similar structure data	4d40-2 3uxw-2 4d40-1 2jab-2 3uxw-1 3uxw-3 2hkb-d 2lho-d 4us7-1 1m1s-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: FLOWER-SPECIFIC DEFENSIN

B: FLOWER-SPECIFIC DEFENSIN

hetero molecules

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

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	33.091, 33.091, 128.770
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	154
Space group name H-M	P3₂21

Components on special symmetry positions

ID	Model	Components
1	1	B-2001- HOH

#1: Protein/peptide	FLOWER-SPECIFIC DEFENSIN / NAD1 Mass: 5315.377 Da / Num. of mol.: 2 / Fragment: RESIDUES 26-72 / Source method: isolated from a natural source / Source: (natural) NICOTIANA ALATA (Persian tobacco) / Organ: FLOWER / References: UniProt: Q8GTM0
#2: Chemical	ChemComp-PO4 / PHOSPHATE ION Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO₄
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 76 / Source method: isolated from a natural source / Formula: H₂O
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: 1.91 Å³/Da / Density % sol: 35.75 % Description: MR PERFORMED WITH ALTERNATIVE CRYSTAL FORM THAT WAS SOLVED BY SIRAS
Crystal grow	pH: 9 Details: 21% (W/V) PEG 1500, 10% (V/V) SUCCINATE-PHOSPHATE-GLYCINE BUFFER, PH 9.15

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.95
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 8, 2011
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.95 Å / Relative weight: 1
Reflection	Resolution: 1.64→42.94 Å / Num. obs: 10797 / % possible obs: 99.1 % / Observed criterion σ(I): 2 / Redundancy: 9.4 % / B_iso Wilson estimate: 18.18 Å² / R_merge(I) obs: 0.08 / Net I/σ(I): 16.4
Reflection shell	Resolution: 1.64→1.72 Å / Redundancy: 5.5 % / R_merge(I) obs: 0.48 / Mean I/σ(I) obs: 3.1 / % possible all: 93.7

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Processing

Software

Name	Version	Classification
PHENIX	(PHENIX.REFINE)	refinement
XDS		data reduction
SCALA		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.636→42.923 Å / SU ML: 0.27 / σ(F): 1.38 / Phase error: 18.77 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2318	516	4.8 %
R_work	0.2064	-	-
obs	0.2075	10677	98.98 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 37.817 Å² / k_sol: 0.363 e/Å³

Displacement parameters

B_iso mean: 20.9 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	5.4232 Å²	0 Å²	0 Å²
2-	-	5.4232 Å²	0 Å²
3-	-	-	10.1898 Å²

Refinement step

Cycle: LAST / Resolution: 1.636→42.923 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	691	0	10	76	777

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	747
X-RAY DIFFRACTION	f_angle_d	1.294	993
X-RAY DIFFRACTION	f_dihedral_angle_d	13.137	289
X-RAY DIFFRACTION	f_chiral_restr	0.065	115
X-RAY DIFFRACTION	f_plane_restr	0.006	124

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 (%)
1.6363-1.801	0.2965	139	0.2443	2359	X-RAY DIFFRACTION	96
1.801-2.0616	0.2587	132	0.1993	2528	X-RAY DIFFRACTION	100
2.0616-2.5974	0.2087	121	0.1901	2552	X-RAY DIFFRACTION	100
2.5974-42.9381	0.2214	124	0.2096	2722	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	9.0071	0.6877	4.214	4.6266	1.0945	2.0002	-0.1568	0.0501	-0.0583	-0.2108	0.1814	0.5338	0.1707	-0.6535	-0.0282	0.2125	0.0589	-0.0573	0.2374	0.0014	0.1014	-21.0593	8.5458	11.7178
2	1.1694	0.2278	-0.3425	0.5763	0.8344	1.9026	0.0063	-0.0323	-0.0012	0.0472	-0.0011	0.0003	0.0125	0.018	-0.0072	-0.0064	0.0382	-0.0122	0.1118	-0.0623	0.0808	-13.05	14.4167	19.4573
3	6.0564	0.6794	-2.1739	1.8371	-0.3714	3.3844	-0.0184	-0.2922	-0.1289	0.1115	0.001	-0.1164	0.0944	0.1754	0.014	0.0998	0.0377	-0.0123	0.1988	-0.0527	0.1158	-18.0459	15.8473	27.9017
4	3.6148	0.6906	-1.8767	3.5841	-0.4066	2.6093	0.011	-0.0206	0.1595	-0.0037	0.018	0.1254	-0.1329	-0.15	-0.0129	0.0559	0.0427	0.0074	0.0985	-0.024	0.1243	-22.9255	19.3692	21.5916
5	6.1481	-1.8924	-1.2101	2.6989	-1.2172	4.4017	0.0677	-0.0709	0.2862	-0.0393	0.0317	-0.0708	-0.2867	0.0635	-0.098	0.057	0.0079	0.0211	0.1052	0.0037	0.1107	-17.0926	20.4732	15.5395
6	2.0276	-0.9867	-0.8737	1.6598	-1.8315	5.7498	0.0702	0.124	0.1329	-0.0285	0.0276	0.0743	-0.1536	-0.1167	-0.1052	0.0521	0.0182	-0.0036	0.1161	-0.0154	0.0561	-21.4366	16.3221	13.8306
7	3.4052	-1.2006	0.7146	1.197	-1.8537	3.966	-0.0726	-0.2731	-0.3521	0.2729	0.0123	0.1744	0.2056	-0.1568	0.0439	0.1689	0.0157	0.0407	0.1174	0.0548	0.1221	-21.806	7.7503	26.8493
8	1.461	0.4246	1.7749	0.4121	-0.0759	4.1119	0.0925	0.225	-0.0621	-0.2182	-0.0527	0.0787	0.1796	0.253	-0.0388	0.0387	0.0958	-0.061	0.1223	0.0144	0.0449	-20.1986	11.4553	12.9359
9	1.4639	0.9092	-1.0856	4.2303	-4.4237	5.4184	-0.065	-0.1039	-0.1814	0.0243	0.0813	0.1167	0.1332	-0.206	-0.0247	0.2371	-0.0628	0.0185	0.133	0.0277	0.0992	-16.7014	5.1839	10.4162
10	3.5631	1.4002	0.0073	3.649	1.7094	3.103	-0.0986	0.2695	0.0794	-0.2646	0.0137	0.1692	-0.1661	-0.0646	0.0874	0.1539	-0.1129	0.0302	0.0249	0.0028	0.0403	-10.0851	9.7095	-1.434
11	2.7403	0.5036	-0.6177	3.8927	1.1844	1.5731	0.0343	0.1655	-0.0128	-0.2464	-0.0311	0.1118	-0.0049	-0.0451	-0.0016	0.2019	-0.0598	-0.006	0.1659	-0.077	0.0898	-13.8645	0.8219	-4.9498
12	2.4968	-1.2065	0.9875	3.5319	0.7977	4.5639	0.0214	0.0395	-0.2322	-0.0646	0.0131	-0.1267	0.1904	0.0304	-0.0339	0.0559	-0.0374	0.0498	0.0639	-0.0232	0.1215	-8.3288	0.8178	1.8034
13	2.5822	1.4313	-0.6922	7.748	-2.0961	3.7745	0.0089	-0.1378	-0.0868	0.0978	-0.0079	-0.194	0.0275	0.2098	0.0003	0.0498	0.0059	-0.0303	0.1119	0.0069	0.1854	-6.7868	2.925	8.1442
14	4.0782	1.9364	0.2223	1.8458	1.6207	2.4899	0.0663	0.0579	-0.0997	-0.1337	0.0087	0.1606	0.0555	-0.0642	-0.0911	0.1187	-0.0154	0.0003	0.0125	-0.0411	0.048	-17.6677	2.1517	0.8956
15	3.5334	-2.15	2.6334	3.3099	-0.1415	3.0262	-0.083	-0.1616	0.3545	-0.2359	0.0459	0.3367	-0.4333	-0.2776	0.0465	0.1958	-0.0211	-0.0698	0.0822	0.0101	0.1489	-19.8466	9.4805	-1.4897
16	0.5654	-0.3213	0.0861	1.689	-3.456	7.721	0.0137	-0.2108	-0.0345	0.2785	-0.0917	-0.1742	-0.1176	0.1975	0.0785	0.1399	-0.0695	-0.0403	0.0477	0.0528	0.0635	-13.9208	2.4146	10.9876

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	(CHAIN A AND RESID 1:5)
2	X-RAY DIFFRACTION	2	(CHAIN A AND RESID 6:10)
3	X-RAY DIFFRACTION	3	(CHAIN A AND RESID 11:16)
4	X-RAY DIFFRACTION	4	(CHAIN A AND RESID 17:21)
5	X-RAY DIFFRACTION	5	(CHAIN A AND RESID 22:27)
6	X-RAY DIFFRACTION	6	(CHAIN A AND RESID 28:33)
7	X-RAY DIFFRACTION	7	(CHAIN A AND RESID 34:39)
8	X-RAY DIFFRACTION	8	(CHAIN A AND RESID 40:47)
9	X-RAY DIFFRACTION	9	(CHAIN B AND RESID 1:6)
10	X-RAY DIFFRACTION	10	(CHAIN B AND RESID 7:13)
11	X-RAY DIFFRACTION	11	(CHAIN B AND RESID 14:19)
12	X-RAY DIFFRACTION	12	(CHAIN B AND RESID 20:25)
13	X-RAY DIFFRACTION	13	(CHAIN B AND RESID 26:30)
14	X-RAY DIFFRACTION	14	(CHAIN B AND RESID 31:36)
15	X-RAY DIFFRACTION	15	(CHAIN B AND RESID 37:41)
16	X-RAY DIFFRACTION	16	(CHAIN B AND RESID 42:47)

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