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- PDB-4l2j: Crystal Structure of Osmotin, an antifungal laticifer protein -

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Basic information

Entry
Database: PDB / ID: 4l2j
TitleCrystal Structure of Osmotin, an antifungal laticifer protein
ComponentsOsmotin: antifungal laticifer protein
KeywordsANTIFUNGAL PROTEIN / Osmotin-like proteins / laticifer proteins / pathogen related protein
Function / homology
Function and homology information


Thaumatin / Thaumatin / Thaumatin, conserved site / Thaumatin family signature. / Thaumatin family / Thaumatin family / Thaumatin family profile. / Thaumatin family / Osmotin/thaumatin-like superfamily / Sandwich / Mainly Beta
Similarity search - Domain/homology
Osmotin: antifungal laticifer protein
Similarity search - Component
Biological speciesCalotropis procera (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.61 Å
AuthorsMoreno, F.B.M.B. / de Oliveira, R.S.B. / de Azevedo Moreira, R. / Lobo, M.D.P. / de Freitas, C.D.T. / Ramos, M.V. / Grangeiro, T.B. / Brandao Neto, J. / D'Muniz Pereira, H. / Monteiro-Moreira, A.C.O.
CitationJournal: To be Published
Title: Crystal Structure of an antifungal laticifer protein
Authors: Moreno, F.B.M.B. / de Oliveira, R.S.B. / de Azevedo Moreira, R. / Lobo, M.D.P. / de Freitas, C.D.T. / Ramos, M.V. / Grangeiro, T.B. / Monteiro-Moreira, A.C.O.
History
DepositionJun 4, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 4, 2014Provider: repository / Type: Initial release
Revision 1.1Jun 11, 2014Group: Derived calculations
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Osmotin: antifungal laticifer protein


Theoretical massNumber of molelcules
Total (without water)22,3781
Polymers22,3781
Non-polymers00
Water3,459192
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)95.590, 95.590, 79.200
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-480-

HOH

Detailsmonomer is observed in solution

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Components

#1: Protein Osmotin: antifungal laticifer protein


Mass: 22377.971 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: laticifer protein / Source: (natural) Calotropis procera (plant) / References: UniProt: A0A067XG70*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 192 / 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: 2.34 Å3/Da / Density % sol: 47.35 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1 M HEPES buffer , 35% MPD, 0.7 M ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 298K, pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 1.608 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL
RadiationMonochromator: Toroidal Grating Monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.608 Å / Relative weight: 1
ReflectionResolution: 1.61→29.101 Å / Num. obs: 25540 / % possible obs: 87.9 % / Observed criterion σ(F): 1.8 / Observed criterion σ(I): 1.8
Reflection shellResolution: 1.8→1.9 Å / % possible all: 83.6

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Processing

Software
NameVersionClassification
MAR345data collection
AMoREphasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.61→29.101 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.911 / SU ML: 0.15 / σ(F): 1.34 / Phase error: 21.84 / Stereochemistry target values: ML / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflection
Rfree0.2159 1416 5.03 %
Rwork0.1812 --
obs0.1829 25540 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 23.271 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å2-0 Å2-0 Å2
2---0.03 Å2-0 Å2
3---0.05 Å2
Refinement stepCycle: LAST / Resolution: 1.61→29.101 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1557 0 0 192 1749
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071614
X-RAY DIFFRACTIONf_angle_d1.1752190
X-RAY DIFFRACTIONf_dihedral_angle_d12.361578
X-RAY DIFFRACTIONf_chiral_restr0.086225
X-RAY DIFFRACTIONf_plane_restr0.006298
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6102-1.66770.25621270.22492622X-RAY DIFFRACTION100
1.6677-1.73450.24291350.20642611X-RAY DIFFRACTION100
1.7345-1.81340.23441500.19372606X-RAY DIFFRACTION100
1.8134-1.9090.20961350.18062646X-RAY DIFFRACTION100
1.909-2.02860.18181210.17132655X-RAY DIFFRACTION100
2.0286-2.18510.19811510.17022631X-RAY DIFFRACTION100
2.1851-2.40490.21311540.17582652X-RAY DIFFRACTION100
2.4049-2.75270.22221420.18452692X-RAY DIFFRACTION100
2.7527-3.46720.22331590.17652706X-RAY DIFFRACTION100
3.4672-29.10530.21371420.18162894X-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)
14.0975-0.5052-1.99130.21530.30790.9794-0.18010.2912-0.549-0.0158-0.01030.01170.0858-0.12590.1830.2035-0.020.05980.2031-0.03680.3165-0.813325.4011-6.3004
21.84660.1015-0.79631.18270.09272.0536-0.22030.45-0.9092-0-0.01780.16360.2821-0.18770.30190.232-0.02390.1040.2029-0.04850.418-3.665720.5773-5.7798
31.48111.0479-0.40490.88180.17560.6844-0.13550.0722-1.37270.3862-0.08210.07520.39120.12750.13520.27720.01330.08710.15990.11830.43290.370421.45652.8909
41.5846-0.2267-1.60822.5379-0.06022.3857-0.3844-0.582-0.7070.46850.0777-0.39490.31970.12160.41620.3470.04080.00770.32410.18860.4734.864820.11835.817
52.5698-0.1727-1.11950.77540.52930.1708-0.0651-0.2319-0.24680.1385-0.02930.08010.00080.11380.08910.1811-0.00010.01740.22550.02230.1915-4.528335.00223.2304
64.7614-4.7248-3.21546.49661.07274.58160.09320.42530.3076-0.3755-0.22340.6591-0.657-0.1556-0.00250.24830.0196-0.05450.24470.01430.2661-13.703442.32-4.5966
72.7231-0.0937-0.40590.8412-0.19530.130.162-0.5777-0.03120.1326-0.0253-0.14270.12580.0808-0.10010.1966-0.0216-0.02110.3592-0.01460.233112.389738.83254.4749
82.657-0.732-0.38932.0110.46512.08010.1141-0.73470.31230.3940.08060.0054-0.28840.2374-0.18710.2764-0.02870.01730.4043-0.08130.28878.520946.45018.2952
92.96640.36692.39142.33371.72532.83640.2439-0.78430.87490.2362-0.07810.483-0.9931-0.6662-0.18170.356-0.00920.07030.4196-0.06990.3231-0.28645.24575.4975
100.12310.11780.06110.24240.0959-0.019-0.09630.159-0.22590.0237-0.06040.08710.03880.00850.12030.1807-0.00230.02640.2426-0.00870.2571-8.937835.0083-4.5575
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 2:19 )A2 - 19
2X-RAY DIFFRACTION2( CHAIN A AND RESID 20:35 )A20 - 35
3X-RAY DIFFRACTION3( CHAIN A AND RESID 36:58 )A36 - 58
4X-RAY DIFFRACTION4( CHAIN A AND RESID 59:76 )A59 - 76
5X-RAY DIFFRACTION5( CHAIN A AND RESID 77:112 )A77 - 112
6X-RAY DIFFRACTION6( CHAIN A AND RESID 113:122 )A113 - 122
7X-RAY DIFFRACTION7( CHAIN A AND RESID 123:156 )A123 - 156
8X-RAY DIFFRACTION8( CHAIN A AND RESID 157:174 )A157 - 174
9X-RAY DIFFRACTION9( CHAIN A AND RESID 175:189 )A175 - 189
10X-RAY DIFFRACTION10( CHAIN A AND RESID 190:206 )A190 - 206

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