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- PDB-1ljp: Crystal Structure of beta-Cinnamomin Elicitin -

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Basic information

Entry
Database: PDB / ID: 1ljp
TitleCrystal Structure of beta-Cinnamomin Elicitin
ComponentsBeta-elicitin cinnamomin
KeywordsTOXIN / elicitin / sterol carrier protein / phytopathogen
Function / homology
Function and homology information


symbiont-mediated perturbation of host programmed cell death / symbiont-mediated killing of host cell / lipid transport / steroid binding / extracellular region
Similarity search - Function
Beta-cryptogein / Elicitin domain / Elicitin / Elicitin superfamily / Elicitin / Elicitin / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Beta-elicitin cinnamomin
Similarity search - Component
Biological speciesPhytophthora cinnamomi (eukaryote)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsRodrigues, M.L. / Archer, M. / Martel, P. / Jacquet, A. / Cravador, A. / Carrondo, M.A.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2002
Title: Structure of beta-cinnamomin, a protein toxic to some plant species.
Authors: Rodrigues, M.L. / Archer, M. / Martel, P. / Jacquet, A. / Cravador, A. / Carrondo, M.A.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2000
Title: Crystallization and preliminary X-ray diffraction analysis of beta-cinnamomin, an elicitin secreted by the phytopathogenic fungus Phytophthora cinnamomin
Authors: Archer, M. / Rodrigues, M.L. / Aurelio, M. / Biemans, R. / Cravador, A. / Carrondo, M.A.
#2: Journal: DNA Seq. / Year: 1998
Title: Identification of an elicitin gene cluster in Phytophthora cinnamomi
Authors: Duclos, J. / Fauconnier, A. / Coelho, A.C. / Bollen, A. / Cravador, A. / Godfroid, E.
History
DepositionApr 22, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 31, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 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
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Beta-elicitin cinnamomin
B: Beta-elicitin cinnamomin


Theoretical massNumber of molelcules
Total (without water)20,6002
Polymers20,6002
Non-polymers00
Water3,621201
1
A: Beta-elicitin cinnamomin


Theoretical massNumber of molelcules
Total (without water)10,3001
Polymers10,3001
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Beta-elicitin cinnamomin


Theoretical massNumber of molelcules
Total (without water)10,3001
Polymers10,3001
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)31.850, 36.910, 43.930
Angle α, β, γ (deg.)77.64, 86.67, 79.55
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Beta-elicitin cinnamomin


Mass: 10299.760 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Phytophthora cinnamomi (eukaryote) / Gene: cin1B / Plasmid: pIC9K / Production host: Pichia pastoris (fungus) / Strain (production host): SMD1168 / References: UniProt: P15569
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 201 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.41 Å3/Da / Density % sol: 42.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: PEG 3350, butanol, ammonium sulfate, Tris-HCl, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 115 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR571 / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 20, 2000
RadiationMonochromator: Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→21.4 Å / Num. all: 16756 / Num. obs: 16756 / % possible obs: 94.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Biso Wilson estimate: 19 Å2 / Rmerge(I) obs: 0.036 / Net I/σ(I): 31.2
Reflection shellResolution: 1.8→1.86 Å / Rmerge(I) obs: 0.121 / Mean I/σ(I) obs: 10.5 / Num. unique all: 1606 / % possible all: 90.3
Reflection
*PLUS
Num. measured all: 61726
Reflection shell
*PLUS
% possible obs: 90.3 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS0.9refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1BEO

1beo


Resolution: 1.8→21.4 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.219 848 5 %RANDOM
Rwork0.198 ---
all0.199 16756 --
obs0.199 16756 94.3 %-
Solvent computationBsol: 94.02 Å2 / ksol: 0.588315 e/Å3
Displacement parametersBiso mean: 18.8 Å2
Baniso -1Baniso -2Baniso -3
1-0.756 Å2-2.391 Å22.411 Å2
2---0.776 Å21.379 Å2
3---0.02 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.23 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.19 Å0.13 Å
Refinement stepCycle: LAST / Resolution: 1.8→21.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1428 0 0 201 1629
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.004
X-RAY DIFFRACTIONc_dihedral_angle_d19.092
X-RAY DIFFRACTIONc_improper_angle_d0.652
X-RAY DIFFRACTIONc_angle_deg1.043
X-RAY DIFFRACTIONc_mcbond_it0.811.5
X-RAY DIFFRACTIONc_scbond_it1.4972
X-RAY DIFFRACTIONc_mcangle_it1.2712
X-RAY DIFFRACTIONc_scangle_it2.1472.5
LS refinement shellResolution: 1.8→1.86 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.29 90 0.05 %
Rwork0.253 1469 -
obs--87.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top
Refinement
*PLUS
Highest resolution: 1.8 Å / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg19.092
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.652
LS refinement shell
*PLUS
Rfactor Rfree: 0.29

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