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- PDB-1beo: BETA-CRYPTOGEIN -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 1beo
TitleBETA-CRYPTOGEIN
ComponentsBETA-CRYPTOGEIN
KeywordsFUNGAL TOXIC ELICITOR / ELICITIN / TOXIN / PLANT PATHOGEN
Function / homology
Function and homology information


symbiont-mediated perturbation of host defense-related programmed cell death / symbiont-mediated killing of host cell / extracellular region
Similarity search - Function
Beta-cryptogein / Elicitin domain / Elicitin / Elicitin superfamily / Elicitin / Elicitin / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Beta-elicitin cryptogein
Similarity search - Component
Biological speciesPhytophthora cryptogea (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD, NATIVE DATA / Resolution: 2.2 Å
AuthorsBoissy, G. / De La Fortelle, E. / Kahn, R. / Huet, J.C. / Bricogne, G. / Pernollet, J.C. / Brunie, S.
Citation
Journal: Structure / Year: 1996
Title: Crystal structure of a fungal elicitor secreted by Phytophthora cryptogea, a member of a novel class of plant necrotic proteins.
Authors: Boissy, G. / de La Fortelle, E. / Kahn, R. / Huet, J.C. / Bricogne, G. / Pernollet, J.C. / Brunie, S.
#1: Journal: J.Mol.Biol. / Year: 1993
Title: Crystallization and Preliminary X-Ray Diffraction Studies of Beta-Cryptogein, a Toxic Elicitin Secreted by the Phytopathogenic Fungus Phytophthora Cryptogea
Authors: Guilloteau, J.P. / Nespoulous, C. / Huet, J.C. / Beauvais, F. / Pernollet, J.C. / Brunie, S.
History
DepositionAug 2, 1996Processing site: BNL
Revision 1.0May 15, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 30, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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: BETA-CRYPTOGEIN


Theoretical massNumber of molelcules
Total (without water)10,3411
Polymers10,3411
Non-polymers00
Water1,18966
1
A: BETA-CRYPTOGEIN

A: BETA-CRYPTOGEIN


Theoretical massNumber of molelcules
Total (without water)20,6822
Polymers20,6822
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_554y,x,-z-1/41
Unit cell
Length a, b, c (Å)46.510, 46.510, 134.900
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number91
Space group name H-MP4122

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Components

#1: Protein BETA-CRYPTOGEIN / BETA-ELICITIN OF PHYTOPHTHORA CRYPTOGEA


Mass: 10340.815 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Phytophthora cryptogea (eukaryote) / References: UniProt: P15570
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 66 / 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: 3.7 Å3/Da / Density % sol: 66 %
Description: PHASING: 4 WAVELENGTHS MAD DATA COLLECTION IN THE VICINITY OF THE PLATINUM LIII ABSORPTION EDGE (ESRF D2AM, 26-08-95).
Crystal growpH: 7.5 / Details: 4.85 M NACL, PH 7.5
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop / Details: used to seeding / PH range low: 10 / PH range high: 4
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
175 mg/mlprotein1drop
20.02 %1dropNaN3
310 mM1dropNaCl
44.85 M1reservoirNaCl
550 mMsodium acetate1reservoir
650 mMTris-HCl1reservoircan be replaced by 50mM CAPS

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: SYNCHROTRON / Site: LURE / Beamline: DW32 / Wavelength: 0.9
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 22, 1995
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionNum. obs: 7864 / % possible obs: 97.2 % / Observed criterion σ(I): 3 / Redundancy: 3.1 % / Biso Wilson estimate: 38 Å2 / Rsym value: 0.032
Reflection
*PLUS
Highest resolution: 2.2 Å / Num. measured all: 35101 / Rmerge(I) obs: 0.032
Reflection shell
*PLUS
Rmerge(I) obs: 0.15

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SHARPphasing
X-PLOR3.1model building
X-PLOR3.1refinement
X-PLOR3.1phasing
RefinementMethod to determine structure: MAD, NATIVE DATA / Resolution: 2.2→7 Å / σ(F): 2
RfactorNum. reflection% reflection
Rfree0.279 -7.5 %
Rwork0.218 --
obs0.218 6987 -
Displacement parametersBiso mean: 37.3 Å2
Refinement stepCycle: LAST / Resolution: 2.2→7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms717 0 0 66 783
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.013
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.5
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Num. reflection all: 7583 / Num. reflection Rfree: 596
Solvent computation
*PLUS
Displacement parameters
*PLUS

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