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

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Basic information

Entry
Database: PDB / ID: 4aaz
TitleX-ray structure of Nicotiana alata Defensin 1 NaD1
ComponentsFLOWER-SPECIFIC DEFENSIN
KeywordsANTIMICROBIAL 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
Defensin, plant / Gamma-thionins family signature. / Gamma-thionin family / Knottins / Knottin, scorpion toxin-like / Knottin, scorpion toxin-like / Knottin, scorpion toxin-like superfamily / Defensin A-like / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Flower-specific defensin
Similarity search - Component
Biological speciesNICOTIANA ALATA (Persian tobacco)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 1.4 Å
AuthorsLay, F.T. / Mills, G.D. / Hulett, M.D. / Kvansakul, M.
CitationJournal: 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
DepositionDec 6, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 25, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 20, 2012Group: Other
Revision 1.2Aug 8, 2012Group: Derived calculations

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: FLOWER-SPECIFIC DEFENSIN
B: FLOWER-SPECIFIC DEFENSIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,0368
Polymers10,6312
Non-polymers4056
Water2,234124
1
A: FLOWER-SPECIFIC DEFENSIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,5975
Polymers5,3151
Non-polymers2814
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: FLOWER-SPECIFIC DEFENSIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,4403
Polymers5,3151
Non-polymers1242
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
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 number4
Space group name H-MP1211

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Components

#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


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 124 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.07 Å3/Da / Density % sol: 40.65 % / Description: NONE
Crystal growpH: 9
Details: 20% PEG 1500 AND 10% SUCCINATE-PHOSPHATE-GLYCINE BUFFER PH 9

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.95
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 8, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95 Å / Relative weight: 1
ReflectionResolution: 1.4→41.23 Å / Num. obs: 17174 / % possible obs: 98.6 % / Observed criterion σ(I): 2 / Redundancy: 6.9 % / Biso Wilson estimate: 5.36 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 18.1
Reflection shellResolution: 1.4→1.47 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 4.6 / % possible all: 90.5

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod 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
RfactorNum. reflection% reflection
Rfree0.1371 869 5.1 %
Rwork0.121 --
obs0.1218 17171 98.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 56.25 Å2 / ksol: 0.413 e/Å3
Displacement parametersBiso mean: 8.9 Å2
Baniso -1Baniso -2Baniso -3
1-1.092 Å20 Å2-1.0802 Å2
2---0.4711 Å20 Å2
3----0.4175 Å2
Refinement stepCycle: LAST / Resolution: 1.4→41.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms728 0 25 124 877
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011777
X-RAY DIFFRACTIONf_angle_d1.5141023
X-RAY DIFFRACTIONf_dihedral_angle_d12.971312
X-RAY DIFFRACTIONf_chiral_restr0.1114
X-RAY DIFFRACTIONf_plane_restr0.01129
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4-1.48770.20341490.16862540X-RAY DIFFRACTION94
1.4877-1.60260.13231260.11522730X-RAY DIFFRACTION100
1.6026-1.76390.1331580.10252719X-RAY DIFFRACTION100
1.7639-2.01910.11051480.10222745X-RAY DIFFRACTION100
2.0191-2.54380.11751520.10442748X-RAY DIFFRACTION100
2.5438-41.24750.14971360.13812820X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°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)
15.8386-4.503-3.72794.19182.4062.7088-0.0919-0.1110.00330.1632-0.00240.0979-0.05350.00760.09340.06830.0078-0.00480.0667-0.00190.05698.14529.092410.0685
21.5589-0.4437-0.16172.27770.51471.9976-0.0003-0.035-0.017-0.01890.0842-0.07590.06430.0238-0.03380.02550.00290.00120.01890.00040.034314.4611-0.98360.7191
32.16220.87970.49481.4952-0.71611.73960.0110.0661-0.12160.0562-0.0743-0.43380.07280.15580.09310.03110.01160.00290.0410.00970.075422.15473.834-3.1261
42.73841.3043-0.75921.8696-0.47612.0844-0.09260.02580.1491-0.02570.0781-0.0976-0.00960.07460.01770.02680.0028-0.00420.02140.0040.048214.89348.5654-4.9806
55.16951.63470.45866.6015-1.60381.9383-0.05660.0402-0.1574-0.26410.0793-0.01610.0595-0.0137-0.00760.02520.0039-0.00410.0163-0.00770.01888.73843.0091-3.7156
67.41381.04131.14842.37860.08763.04140.0340.00860.01070.0336-0.02360.03060.0355-0.06660.04540.01230.0018-0.00410.0125-0.0110.02838.77617.22051.1416
75.32640.66213.32132.9473-1.68215.7593-0.0874-0.00650.26350.2408-0.1953-0.4316-0.22710.29510.04290.0435-0.0147-0.02090.07020.0010.076424.48176.84844.5787
82.5409-1.454-1.37620.84060.64831.69160.01340.046-0.00630.0737-0.0391-0.00320.0314-0.09260.03170.0362-0.0032-0.00670.0211-0.0060.041510.856.29585.8261
92.49130.9204-0.86221.7262-0.68060.7816-0.1994-0.4428-0.45810.34280.0690.54970.1365-0.3402-0.27570.1446-0.00510.11670.11820.09140.1396-3.2847.0396-11.6853
101.3363-0.492-0.92583.77621.58784.15980.00370.09640.0855-0.22390.0494-0.0114-0.1089-0.0174-0.0580.05290.00220.00020.01550.00380.03875.426515.47-21.3036
113.7257-1.94472.73871.3497-0.59914.54160.0597-0.0145-0.1125-0.01380.0650.02790.0180.0408-0.06980.0574-0.00250.00250.026-0.00540.03677.88276.4963-24.5456
123.1308-1.17351.85075.03413.51477.59440.03350.09960.0540.11320.1446-0.31840.15670.2604-0.11120.0372-0.0011-0.01550.0140.00240.0489.49028.5492-16.325
131.81850.4146-0.58441.3734-0.36061.48870.0555-0.01160.10890.09960.0166-0.0743-0.1081-0.0453-0.0730.07110.004-0.0190.0295-0.00740.03026.664310.9002-10.1372
144.45140.78363.42742.26481.9793.51560.23690.087-0.1278-0.024-0.04280.16060.54820.0288-0.49630.07520.0176-0.0410.01490.01060.02961.67454.6556-20.5393
152.42821.1872.36884.90762.21956.2384-0.0839-0.03860.1424-0.2232-0.09790.3397-0.2353-0.38630.10570.0460.0192-0.01730.0571-0.00620.0555-1.842810.2372-25.7402
163.7273-0.0862-0.4172.9239-1.64314.07860.1183-0.48170.01460.23440.00440.3159-0.0668-0.1537-0.09820.0585-0.0025-0.01260.05420.01030.050.59226.4031-10.4351
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 1:5)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 6:10)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 11:16)
4X-RAY DIFFRACTION4(CHAIN A AND RESID 17:21)
5X-RAY DIFFRACTION5(CHAIN A AND RESID 22:27)
6X-RAY DIFFRACTION6(CHAIN A AND RESID 28:33)
7X-RAY DIFFRACTION7(CHAIN A AND RESID 34:39)
8X-RAY DIFFRACTION8(CHAIN A AND RESID 40:47)
9X-RAY DIFFRACTION9(CHAIN B AND RESID 1:6)
10X-RAY DIFFRACTION10(CHAIN B AND RESID 7:13)
11X-RAY DIFFRACTION11(CHAIN B AND RESID 14:19)
12X-RAY DIFFRACTION12(CHAIN B AND RESID 20:25)
13X-RAY DIFFRACTION13(CHAIN B AND RESID 26:30)
14X-RAY DIFFRACTION14(CHAIN B AND RESID 31:36)
15X-RAY DIFFRACTION15(CHAIN B AND RESID 37:41)
16X-RAY DIFFRACTION16(CHAIN B AND RESID 42:47)

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