PDB-4aaz: X-ray structure of Nicotiana alata Defensin 1 NaD1

ID or keywords:

Entry

Database: PDB / ID: 4aaz

Title

X-ray structure of Nicotiana alata Defensin 1 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 /

SIRAS / Resolution: 1.4 Å

Authors

Lay, F.T. / Mills, G.D. / 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	Aug 8, 2012	Group: Derived calculations

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	4aaz.cif.gz	50.9 KB	Display	PDBx/mmCIF format
PDB format	pdb4aaz.ent.gz	42 KB	Display	PDB format
PDBx/mmJSON format	4aaz.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/aa/4aaz ftp://data.pdbj.org/pub/pdb/validation_reports/aa/4aaz	HTTPS FTP

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Related structure data

Related structure data	4ab0C C: citing same article (ref.)
Similar structure data	3szs-6 2lj7-d 4rof-2 2ly5-d 5wlx-d 2ysh-d 2lep-d 4w71-1 7c2p-2 2laz-d 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
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

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

1

A: FLOWER-SPECIFIC DEFENSIN

hetero molecules

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

2

B: FLOWER-SPECIFIC DEFENSIN

hetero molecules

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

Unit cell

Length a, b, c (Å)	32.697, 32.685, 41.977
Angle α, β, γ (deg.)	90.00, 100.83, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#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) / References: UniProt: Q8GTM0
#2: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C₂H₆O₂
#3: Chemical	ChemComp-PO4 / PHOSPHATE ION / Phosphate Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO₄
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 124 / 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: 2.07 Å³/Da / Density % sol: 40.65 % / Description: NONE
Crystal grow	pH: 9 Details: 20% PEG 1500 AND 10% SUCCINATE-PHOSPHATE-GLYCINE BUFFER PH 9

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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: 1.4→41.23 Å / Num. obs: 17174 / % possible obs: 98.6 % / Observed criterion σ(I): 2 / Redundancy: 6.9 % / B_iso Wilson estimate: 5.36 Å² / R_merge(I) obs: 0.09 / Net I/σ(I): 18.1
Reflection shell	Resolution: 1.4→1.47 Å / Redundancy: 4.8 % / R_merge(I) obs: 0.4 / Mean I/σ(I) obs: 4.6 / % possible all: 90.5

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Processing

Software

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

Refinement

Method to determine structure:

SIRAS
Starting model: NONE

Resolution: 1.4→41.23 Å / SU ML: 0.31 / σ(F): 1.37 / Phase error: 11.25 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1371	869	5.1 %
R_work	0.121	-	-
obs	0.1218	17171	98.96 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 56.25 Å² / k_sol: 0.413 e/Å³

Displacement parameters

B_iso mean: 8.9 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	1.092 Å²	0 Å²	-1.0802 Å²
2-	-	-0.4711 Å²	0 Å²
3-	-	-	-0.4175 Å²

Refinement step

Cycle: LAST / Resolution: 1.4→41.23 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	728	0	25	124	877

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.011	777
X-RAY DIFFRACTION	f_angle_d	1.514	1023
X-RAY DIFFRACTION	f_dihedral_angle_d	12.971	312
X-RAY DIFFRACTION	f_chiral_restr	0.1	114
X-RAY DIFFRACTION	f_plane_restr	0.01	129

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 (%)
1.4-1.4877	0.2034	149	0.1686	2540	X-RAY DIFFRACTION	94
1.4877-1.6026	0.1323	126	0.1152	2730	X-RAY DIFFRACTION	100
1.6026-1.7639	0.133	158	0.1025	2719	X-RAY DIFFRACTION	100
1.7639-2.0191	0.1105	148	0.1022	2745	X-RAY DIFFRACTION	100
2.0191-2.5438	0.1175	152	0.1044	2748	X-RAY DIFFRACTION	100
2.5438-41.2475	0.1497	136	0.1381	2820	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	5.8386	-4.503	-3.7279	4.1918	2.406	2.7088	-0.0919	-0.111	0.0033	0.1632	-0.0024	0.0979	-0.0535	0.0076	0.0934	0.0683	0.0078	-0.0048	0.0667	-0.0019	0.0569	8.1452	9.0924	10.0685
2	1.5589	-0.4437	-0.1617	2.2777	0.5147	1.9976	-0.0003	-0.035	-0.017	-0.0189	0.0842	-0.0759	0.0643	0.0238	-0.0338	0.0255	0.0029	0.0012	0.0189	0.0004	0.0343	14.4611	-0.9836	0.7191
3	2.1622	0.8797	0.4948	1.4952	-0.7161	1.7396	0.011	0.0661	-0.1216	0.0562	-0.0743	-0.4338	0.0728	0.1558	0.0931	0.0311	0.0116	0.0029	0.041	0.0097	0.0754	22.1547	3.834	-3.1261
4	2.7384	1.3043	-0.7592	1.8696	-0.4761	2.0844	-0.0926	0.0258	0.1491	-0.0257	0.0781	-0.0976	-0.0096	0.0746	0.0177	0.0268	0.0028	-0.0042	0.0214	0.004	0.0482	14.8934	8.5654	-4.9806
5	5.1695	1.6347	0.4586	6.6015	-1.6038	1.9383	-0.0566	0.0402	-0.1574	-0.2641	0.0793	-0.0161	0.0595	-0.0137	-0.0076	0.0252	0.0039	-0.0041	0.0163	-0.0077	0.0188	8.7384	3.0091	-3.7156
6	7.4138	1.0413	1.1484	2.3786	0.0876	3.0414	0.034	0.0086	0.0107	0.0336	-0.0236	0.0306	0.0355	-0.0666	0.0454	0.0123	0.0018	-0.0041	0.0125	-0.011	0.0283	8.7761	7.2205	1.1416
7	5.3264	0.6621	3.3213	2.9473	-1.6821	5.7593	-0.0874	-0.0065	0.2635	0.2408	-0.1953	-0.4316	-0.2271	0.2951	0.0429	0.0435	-0.0147	-0.0209	0.0702	0.001	0.0764	24.4817	6.8484	4.5787
8	2.5409	-1.454	-1.3762	0.8406	0.6483	1.6916	0.0134	0.046	-0.0063	0.0737	-0.0391	-0.0032	0.0314	-0.0926	0.0317	0.0362	-0.0032	-0.0067	0.0211	-0.006	0.0415	10.85	6.2958	5.8261
9	2.4913	0.9204	-0.8622	1.7262	-0.6806	0.7816	-0.1994	-0.4428	-0.4581	0.3428	0.069	0.5497	0.1365	-0.3402	-0.2757	0.1446	-0.0051	0.1167	0.1182	0.0914	0.1396	-3.284	7.0396	-11.6853
10	1.3363	-0.492	-0.9258	3.7762	1.5878	4.1598	0.0037	0.0964	0.0855	-0.2239	0.0494	-0.0114	-0.1089	-0.0174	-0.058	0.0529	0.0022	0.0002	0.0155	0.0038	0.0387	5.4265	15.47	-21.3036
11	3.7257	-1.9447	2.7387	1.3497	-0.5991	4.5416	0.0597	-0.0145	-0.1125	-0.0138	0.065	0.0279	0.018	0.0408	-0.0698	0.0574	-0.0025	0.0025	0.026	-0.0054	0.0367	7.8827	6.4963	-24.5456
12	3.1308	-1.1735	1.8507	5.0341	3.5147	7.5944	0.0335	0.0996	0.054	0.1132	0.1446	-0.3184	0.1567	0.2604	-0.1112	0.0372	-0.0011	-0.0155	0.014	0.0024	0.048	9.4902	8.5492	-16.325
13	1.8185	0.4146	-0.5844	1.3734	-0.3606	1.4887	0.0555	-0.0116	0.1089	0.0996	0.0166	-0.0743	-0.1081	-0.0453	-0.073	0.0711	0.004	-0.019	0.0295	-0.0074	0.0302	6.6643	10.9002	-10.1372
14	4.4514	0.7836	3.4274	2.2648	1.979	3.5156	0.2369	0.087	-0.1278	-0.024	-0.0428	0.1606	0.5482	0.0288	-0.4963	0.0752	0.0176	-0.041	0.0149	0.0106	0.0296	1.6745	4.6556	-20.5393
15	2.4282	1.187	2.3688	4.9076	2.2195	6.2384	-0.0839	-0.0386	0.1424	-0.2232	-0.0979	0.3397	-0.2353	-0.3863	0.1057	0.046	0.0192	-0.0173	0.0571	-0.0062	0.0555	-1.8428	10.2372	-25.7402
16	3.7273	-0.0862	-0.417	2.9239	-1.6431	4.0786	0.1183	-0.4817	0.0146	0.2344	0.0044	0.3159	-0.0668	-0.1537	-0.0982	0.0585	-0.0025	-0.0126	0.0542	0.0103	0.05	0.5922	6.4031	-10.4351

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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