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- PDB-6mry: NoD173 plant defensin -

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Basic information

Entry
Database: PDB / ID: 6mry
TitleNoD173 plant defensin
ComponentsNoD173 defensin
KeywordsANTITUMOR PROTEIN / Defensin / Plant / Cancer
Function / homology
Function and homology information


Defensin, plant / Gamma-thionins family signature. / Gamma-thionin family / Knottins / Knottin, scorpion toxin-like / Knottin, scorpion toxin-like superfamily
Similarity search - Domain/homology
CITRATE ANION / Chem-I3C / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / NoD173 defensin
Similarity search - Component
Biological speciesNicotiana occidentalis (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsCaria, S. / Kvansakul, M.
Funding support Australia, 1items
OrganizationGrant numberCountry
Australian Research Council (ARC)FT130101349 Australia
CitationJournal: Faseb J. / Year: 2019
Title: Structural and functional characterization of the membrane-permeabilizing activity ofNicotiana occidentalisdefensin NoD173 and protein engineering to enhance oncolysis.
Authors: Lay, F.T. / Ryan, G.F. / Caria, S. / Phan, T.K. / Veneer, P.K. / White, J.A. / Kvansakul, M. / Hulett, M.D.
History
DepositionOct 15, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 24, 2019Provider: repository / Type: Initial release
Revision 1.1May 15, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 11, 2023Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NoD173 defensin
B: NoD173 defensin
C: NoD173 defensin
D: NoD173 defensin
E: NoD173 defensin
F: NoD173 defensin
G: NoD173 defensin
H: NoD173 defensin
I: NoD173 defensin
J: NoD173 defensin
K: NoD173 defensin
L: NoD173 defensin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,56543
Polymers65,33412
Non-polymers5,23131
Water2,144119
1
A: NoD173 defensin
E: NoD173 defensin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,2386
Polymers10,8892
Non-polymers3494
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2260 Å2
ΔGint-7 kcal/mol
Surface area6340 Å2
MethodPISA
2
B: NoD173 defensin
G: NoD173 defensin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,8598
Polymers10,8892
Non-polymers9706
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2050 Å2
ΔGint-11 kcal/mol
Surface area6650 Å2
MethodPISA
3
C: NoD173 defensin
J: NoD173 defensin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,6995
Polymers10,8892
Non-polymers8103
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2060 Å2
ΔGint2 kcal/mol
Surface area6280 Å2
MethodPISA
4
D: NoD173 defensin
hetero molecules

L: NoD173 defensin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,5828
Polymers10,8892
Non-polymers6936
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area2380 Å2
ΔGint-9 kcal/mol
Surface area5810 Å2
MethodPISA
5
F: NoD173 defensin
I: NoD173 defensin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,2937
Polymers10,8892
Non-polymers1,4045
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2020 Å2
ΔGint-11 kcal/mol
Surface area6030 Å2
MethodPISA
6
H: NoD173 defensin
K: NoD173 defensin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,8949
Polymers10,8892
Non-polymers1,0057
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2020 Å2
ΔGint-31 kcal/mol
Surface area5810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.107, 69.318, 107.662
Angle α, β, γ (deg.)90.00, 108.08, 90.00
Int Tables number5
Space group name H-MI121

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Components

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Protein/peptide , 1 types, 12 molecules ABCDEFGHIJKL

#1: Protein/peptide
NoD173 defensin


Mass: 5444.524 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nicotiana occidentalis (plant) / Production host: Komagataella pastoris (fungus) / References: UniProt: A0A4V8H030*PLUS

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Non-polymers , 7 types, 150 molecules

#2: Chemical
ChemComp-FLC / CITRATE ANION / Citric acid


Mass: 189.100 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C6H5O7
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#5: Chemical
ChemComp-I3C / 5-amino-2,4,6-triiodobenzene-1,3-dicarboxylic acid / 5-Amino-2,4,6-triiodoisophthalic acid


Mass: 558.835 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C8H4I3NO4
#6: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#7: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 119 / 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: 2.59 Å3/Da / Density % sol: 52.49 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 8.6 / Details: Tris-HCl, trisodium citrate, PEG 400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Nov 5, 2014
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.3→45.2 Å / Num. obs: 29667 / % possible obs: 99.7 % / Redundancy: 3.7 % / Biso Wilson estimate: 13.21 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.083 / Rpim(I) all: 0.078 / Net I/σ(I): 11.8
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.561 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 2920 / CC1/2: 0.743 / Rpim(I) all: 0.521 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
xia2data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4AB0

4ab0


Resolution: 2.3→34.37 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.69
RfactorNum. reflection% reflection
Rfree0.2321 1470 4.96 %
Rwork0.1894 --
obs0.1916 29658 99.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.3→34.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4419 0 235 119 4773
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084733
X-RAY DIFFRACTIONf_angle_d1.1616312
X-RAY DIFFRACTIONf_dihedral_angle_d19.4033072
X-RAY DIFFRACTIONf_chiral_restr0.054665
X-RAY DIFFRACTIONf_plane_restr0.006794
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.38220.3441280.24982842X-RAY DIFFRACTION100
2.3822-2.47760.30861490.23232795X-RAY DIFFRACTION100
2.4776-2.59030.28151350.22892784X-RAY DIFFRACTION100
2.5903-2.72680.26631370.22672836X-RAY DIFFRACTION100
2.7268-2.89760.25311550.20352812X-RAY DIFFRACTION100
2.8976-3.12120.29761440.2122800X-RAY DIFFRACTION100
3.1212-3.4350.25411440.18512833X-RAY DIFFRACTION100
3.435-3.93150.20311730.1662772X-RAY DIFFRACTION100
3.9315-4.95090.17911440.14342851X-RAY DIFFRACTION99
4.9509-34.37390.20171610.19452863X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 5.4452 Å / Origin y: -11.4912 Å / Origin z: -19.9287 Å
111213212223313233
T0.1251 Å2-0.0346 Å2-0.0037 Å2-0.1103 Å2-0.0159 Å2--0.1211 Å2
L0.2275 °2-0.0297 °20.1613 °2-0.3489 °20.0121 °2--0.3875 °2
S-0.0144 Å °0.2461 Å °-0.0054 Å °-0.1664 Å °0.047 Å °-0.0984 Å °0.0064 Å °0.1973 Å °0.0264 Å °
Refinement TLS groupSelection details: all

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