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- PDB-2a8f: beta-cinnamomin after sterol removal -

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Basic information

Entry
Database: PDB / ID: 2a8f
Titlebeta-cinnamomin after sterol removal
ComponentsBeta-elicitin cinnamomin
KeywordsTOXIN / elicitin / sterol carrier protein / phytophthora / 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å
AuthorsRodrigues, M.L. / Archer, M. / Martel, P. / Miranda, S. / Thomaz, M. / Enguita, F.J. / Baptista, R.P. / Melo, E.P. / Sousa, N. / Cravador, A. / Carrondo, M.A.
Citation
Journal: Biochim.Biophys.Acta / Year: 2006
Title: Crystal structures of the free and sterol-bound forms of beta-cinnamomin
Authors: Rodrigues, M.L. / Archer, M. / Martel, P. / Miranda, S. / Thomaz, M. / Enguita, F.J. / Baptista, R.P. / Melo, E.P. / Sousa, N. / Cravador, A. / Carrondo, M.A.
#1: 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.
#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
DepositionJul 8, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 17, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 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 1.4Oct 9, 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
Water6,467359
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1040 Å2
ΔGint-11 kcal/mol
Surface area9660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.048, 58.048, 106.656
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-251-

HOH

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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.: 359 / 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: 2.2 Å3/Da / Density % sol: 43.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: PEG 4000, Hepes buffer, MPD, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.933 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 15, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.35→50.99 Å / Num. all: 39554 / Num. obs: 39554 / % possible obs: 97.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.9 % / Rmerge(I) obs: 0.065 / Net I/σ(I): 19
Reflection shellResolution: 1.35→1.38 Å / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 2.9 / % possible all: 91.2

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
SHELXL-97refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1LJP

1ljp


Resolution: 1.35→50.99 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.192 1962 RANDOM
Rwork0.138 --
all0.141 39554 -
obs0.141 39554 -
Displacement parametersBiso mean: 19 Å2
Refinement stepCycle: LAST / Resolution: 1.35→50.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1488 0 0 359 1847
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.014
X-RAY DIFFRACTIONs_angle_d0.028
X-RAY DIFFRACTIONs_from_restr_planes0.327

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