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- PDB-7c31: Crystal structure of the grapevine defensin VvK1 -

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Basic information

Entry
Database: PDB / ID: 7c31
TitleCrystal structure of the grapevine defensin VvK1
ComponentsKnot1 domain-containing protein
KeywordsANTIMICROBIAL PROTEIN / cysteine-rich / antimicrobial / antifungal / immunomodulatory / plant defensin
Function / homologyDefensin, plant / Gamma-thionins family signature. / Gamma-thionin family / Knottins / Knottin, scorpion toxin-like / Knottin, scorpion toxin-like superfamily / defense response to fungus / killing of cells of another organism / Knot1 domain-containing protein
Function and homology information
Biological speciesVitis vinifera (wine grape)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsChen, M.W. / Chang, S.C. / Chandy, K.G. / Luo, D.
CitationJournal: Acs Pharmacol Transl Sci / Year: 2020
Title: Modulation of Lymphocyte Potassium Channel KV1.3 by Membrane-Penetrating, Joint-Targeting Immunomodulatory Plant Defensin.
Authors: Ong, S.T. / Bajaj, S. / Tanner, M.R. / Chang, S.C. / Krishnarjuna, B. / Ng, X.R. / Morales, R.A.V. / Chen, M.W. / Luo, D. / Patel, D. / Yasmin, S. / Ng, J.J.H. / Zhuang, Z. / Nguyen, H.M. / ...Authors: Ong, S.T. / Bajaj, S. / Tanner, M.R. / Chang, S.C. / Krishnarjuna, B. / Ng, X.R. / Morales, R.A.V. / Chen, M.W. / Luo, D. / Patel, D. / Yasmin, S. / Ng, J.J.H. / Zhuang, Z. / Nguyen, H.M. / El Sahili, A. / Lescar, J. / Patil, R. / Charman, S.A. / Robins, E.G. / Goggi, J.L. / Tan, P.W. / Sadasivam, P. / Ramasamy, B. / Hartimath, S.V. / Dhawan, V. / Bednenko, J. / Colussi, P. / Wulff, H. / Pennington, M.W. / Kuyucak, S. / Norton, R.S. / Beeton, C. / Chandy, K.G.
History
DepositionMay 10, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 16, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 29, 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

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Assembly

Deposited unit
A: Knot1 domain-containing protein
B: Knot1 domain-containing protein


Theoretical massNumber of molelcules
Total (without water)10,4762
Polymers10,4762
Non-polymers00
Water1,56787
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)27.854, 27.854, 99.605
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number78
Space group name H-MP43
Space group name HallP4cw
Symmetry operation#1: x,y,z
#2: -y,x,z+3/4
#3: y,-x,z+1/4
#4: -x,-y,z+1/2

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Components

#1: Protein/peptide Knot1 domain-containing protein


Mass: 5238.158 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Vitis vinifera (wine grape) / References: UniProt: F6HGI0
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 87 / 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: 1.84 Å3/Da / Density % sol: 33.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 15% PEG 4000, 0.2M MgCl2, 0.1M Tris-HCl pH 8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Oct 21, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.3→27.85 Å / Num. obs: 18614 / % possible obs: 99.92 % / Redundancy: 4.9 % / Biso Wilson estimate: 12.14 Å2 / CC1/2: 0.988 / Net I/σ(I): 34.87
Reflection shellResolution: 1.3→1.346 Å / Rmerge(I) obs: 0.5795 / Mean I/σ(I) obs: 3.79 / Num. unique obs: 1855 / CC1/2: 0.763 / Rpim(I) all: 0.296 / Rrim(I) all: 0.6516

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Processing

Software
NameVersionClassification
PHENIX1.18_3845refinement
iMOSFLMdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4UJ0

4uj0


Resolution: 1.3→27.85 Å / SU ML: 0.137 / Cross valid method: FREE R-VALUE / σ(F): 1.4 / Phase error: 23.8311
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1898 971 5.22 %
Rwork0.169 17632 -
obs0.1701 18603 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 21.93 Å2
Refinement stepCycle: LAST / Resolution: 1.3→27.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms716 0 0 87 803
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0132742
X-RAY DIFFRACTIONf_angle_d1.6166984
X-RAY DIFFRACTIONf_chiral_restr0.200599
X-RAY DIFFRACTIONf_plane_restr0.0055132
X-RAY DIFFRACTIONf_dihedral_angle_d5.0245110
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3-1.370.27541480.25762501X-RAY DIFFRACTION99.77
1.37-1.450.24111320.22822525X-RAY DIFFRACTION99.89
1.45-1.570.19841620.18512498X-RAY DIFFRACTION99.92
1.57-1.720.17591430.16422513X-RAY DIFFRACTION99.96
1.72-1.970.19541010.17642542X-RAY DIFFRACTION99.96
1.97-2.480.17661210.15952536X-RAY DIFFRACTION100
2.49-27.850.18021640.1522517X-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)
13.17713710271-0.6173862299013.437703180171.95780019064-0.7658190536623.825797306730.0977848716750.293104248481-0.1692998895990.03931179629960.159166386657-0.3647790804080.2466752103760.662733269132-0.1870980884240.1294888735070.0544894989758-0.03167707401830.17311946679-0.05945929093820.174338306936-27.615238743949.7698728912.42576091803
25.721864028042.06540641806-0.8597415497473.77673564601-3.945046446668.22307542458-0.06062932984780.246419319198-0.224805841038-0.2255978771660.1738282913920.353267356241-0.242428536461-0.465758775219-0.1323577771790.1118948007720.0178383205461-0.009011316883020.136290977305-0.009690824316830.17379817581-39.641352660656.7495590471-5.01907446397
34.4312257235-0.226306625557-1.819418953086.58306676603-1.832862104039.01543084597-0.161369743317-0.3613430971520.2103181812010.3130949754440.1454943251120.16513913367-0.2406406695570.07408920106260.04621807751230.1172444457760.0335812996374-0.001717082915750.117958255489-0.0297765477060.112327128858-37.165447023360.77910999962.54630793684
41.24614948066-0.1404655870020.9739185739143.42465634573-0.6714496846449.88471458835-0.073066753536-0.0551154545303-0.01747202834560.2000607295420.1809328663790.09439030173510.03838455086530.0918364290693-0.005971611987920.12122992340.02804288233720.00833704108550.112513937632-0.001361673037460.108086343723-32.978786498455.96489179372.2139132159
52.424066536580.6837236149030.2869845939962.25572118351-0.4855625068065.31397505634-0.05531613456550.0960299116979-0.118149307717-0.07642790622460.0959380296194-0.08297509369510.4953546486760.164970485519-0.04995008363310.1005142779640.03393686306080.01095244680730.0801407117904-0.02710975665520.0865860079156-31.167080219453.7262958821-3.09985006954
68.4671044288-0.909889801756-2.416204507753.552345335360.07191226989362.911519598080.008309978796770.4169928210160.26903155843-0.2088449245640.0267044923203-0.133664249461-0.0340448865137-0.188549286039-0.04657017109320.1432232702840.00717551833559-0.003326521474690.148473408779-0.01429490619390.143673463657-20.025590205542.7375541985-1.00447110748
74.156674096290.151954290551-2.440295084774.32567243030.4578429691876.45549647603-0.149757290817-0.105758609629-0.369174121833-0.09684604674490.05915381694620.03623639724750.1067953030420.03334013697030.09855926652040.06971437787440.0322148764970.01428936354470.1150421790890.008599089171980.119912972783-20.499837356936.97024322651.0064784133
85.270659248530.7280082101-1.303631101764.48704119198-1.625269801611.828361422020.06430900883110.2497980618010.230715748988-0.496522544498-0.04318031975750.167948394833-0.122372093989-0.116187451479-0.03646691322240.1637580667760.0441941154132-0.01502548739310.1322707550860.006698674632090.136664580647-22.388508826143.7172813609-3.30504043656
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 1 through 6 )AZ00A1 - 61 - 6
22chain 'A' and (resid 7 through 16 )AZ00A7 - 167 - 16
33chain 'A' and (resid 17 through 26 )AZ00A17 - 2617 - 28
44chain 'A' and (resid 27 through 35 )AZ00A27 - 3529 - 40
55chain 'A' and (resid 36 through 47 )AZ00A36 - 4741 - 52
66chain 'B' and (resid 1 through 16 )AZZ0B1 - 161 - 18
77chain 'B' and (resid 17 through 35 )AZZ0B17 - 3519 - 37
88chain 'B' and (resid 36 through 47 )AZZ0B36 - 4738 - 49

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