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- PDB-1bxm: ENGINEERED BETA-CRYPTOGEIN COMPLEXED WITH ERGOSTEROL -

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Basic information

Entry
Database: PDB / ID: 1bxm
TitleENGINEERED BETA-CRYPTOGEIN COMPLEXED WITH ERGOSTEROL
ComponentsBETA-CRYPTOGEIN
KeywordsFUNGAL TOXIC ELICITOR / FUNGAL TOXIC ELICITOR MUTANT / ELICITIN / PHYTOPHTHORA / STEROL / 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
ERGOSTEROL / Beta-elicitin cryptogein
Similarity search - Component
Biological speciesPhytophthora cryptogea (eukaryote)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsBoissy, G. / Brunie, S.
Citation
Journal: Protein Sci. / Year: 1999
Title: The 2.1 A structure of an elicitin-ergosterol complex: a recent addition to the Sterol Carrier Protein family.
Authors: Boissy, G. / O'Donohue, M. / Gaudemer, O. / Perez, V. / Pernollet, J.C. / Brunie, S.
#1: 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.
#2: Journal: Protein Expr.Purif. / Year: 1996
Title: Overexpression in Pichia Pastoris and Crystallization of an Elicitor Protein Secreted by the Phytopathogenic Fungus, Phytophthora Cryptogea
Authors: O'Donohue, M.J. / Boissy, G. / Huet, J.C. / Nespoulous, C. / Brunie, S. / Pernollet, J.C.
#3: 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
DepositionOct 5, 1998Processing site: BNL
Revision 1.0Jun 15, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Nov 3, 2021Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Refinement description
Category: atom_site / database_2 ...atom_site / database_2 / software / struct_ref_seq_dif / struct_site
Item: _atom_site.occupancy / _database_2.pdbx_DOI ..._atom_site.occupancy / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _software.name / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.1Aug 9, 2023Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: BETA-CRYPTOGEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,8902
Polymers10,4931
Non-polymers3971
Water1,02757
1
A: BETA-CRYPTOGEIN
hetero molecules

A: BETA-CRYPTOGEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,7794
Polymers20,9862
Non-polymers7932
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Unit cell
Length a, b, c (Å)31.130, 95.230, 65.700
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-101-

HOH

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Components

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


Mass: 10492.951 Da / Num. of mol.: 1 / Mutation: T1G, A2T, K13H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Phytophthora cryptogea (eukaryote)
Description: N-TERMINAL ARGININE INCORPORATION NON-BIOLOGICAL SEQUENCE
Cell line: PICHIA PASTORIS / Gene: CRY (MUTATED LYS 13 HIS) / Plasmid: PHILS1 / Gene (production host): CRY (MUTATED LYS 13 HIS) / Production host: Pichia pastoris (fungus) / References: UniProt: P15570
#2: Chemical ChemComp-ERG / ERGOSTEROL / Ergosterol


Mass: 396.648 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C28H44O
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 57 / 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: 2.3 Å3/Da / Density % sol: 47 %
Crystal growpH: 4.5 / Details: pH 4.5
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
175 mg/mlprotein1drop
23.2-4.9 M1reservoirNaCl
350 mMsodium acetate1reservoir
40.01 %1reservoirNaN3

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 1, 1996
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→10 Å / Num. obs: 5370 / % possible obs: 96.1 % / Observed criterion σ(I): 2 / Redundancy: 6.1 % / Biso Wilson estimate: 20.9 Å2 / Rsym value: 0.046
Reflection
*PLUS
Num. measured all: 33143 / Rmerge(I) obs: 0.046

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Processing

Software
NameVersionClassification
XDSdata scaling
ROTAVATAdata reduction
Agrovatadata reduction
X-PLOR3.851model building
X-PLOR3.851refinement
XDSdata reduction
CCP4(AGROVATAdata scaling
ROTAVATAdata scaling
X-PLOR3.851phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: THE REFINED 2.2 ANGSTROMS RESOLUTION STRUCTURE OF THE WILD-TYPE BETA-CRYPTOGEIN (1BEO). THE ERGOSTEROL MOLECULE WAS CONSTRUCTED USING, AS A TEMPLATE, THE COORDINATES OF THE ...Starting model: THE REFINED 2.2 ANGSTROMS RESOLUTION STRUCTURE OF THE WILD-TYPE BETA-CRYPTOGEIN (1BEO). THE ERGOSTEROL MOLECULE WAS CONSTRUCTED USING, AS A TEMPLATE, THE COORDINATES OF THE CHOLESTERYL LINOLEATE MOLECULE COMPLEXED TO THE CHOLESTEROL ESTERASE (1CLE).

1beo

1cle


Resolution: 2.15→8 Å / Rfactor Rfree error: 0.015 / Data cutoff high absF: 100000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 3 / Details: RESOLUTION-DEPENDENT WEIGHTING SCHEME USED.
RfactorNum. reflection% reflectionSelection details
Rfree0.229 224 4.6 %RANDOM
Rwork0.189 ---
obs0.189 4921 89.8 %-
Displacement parametersBiso mean: 18.6 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.28 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.25 Å0.06 Å
Refinement stepCycle: LAST / Resolution: 2.15→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms726 0 29 57 812
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.009
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_deg1.3
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d22.8
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.65
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.461.5
X-RAY DIFFRACTIONx_mcangle_it2.022
X-RAY DIFFRACTIONx_scbond_it2.392
X-RAY DIFFRACTIONx_scangle_it2.972.5
LS refinement shellResolution: 2.15→2.28 Å / Rfactor Rfree error: 0.052 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.267 26 4 %
Rwork0.157 629 -
obs--72.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMTOPHCSDX.PRO
X-RAY DIFFRACTION2ERG.PARTOPH19.SOL
X-RAY DIFFRACTION3ERG.TOP
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg22.8
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.65

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