1LRI

BETA-CRYPTOGEIN-CHOLESTEROL COMPLEX

PDB DOI: https://doi.org/10.2210/pdb1LRI/pdb

Classification: TOXIN
Organism(s): Phytophthora cryptogea
Mutation(s): No

Deposited: 2002-05-15 Released: 2002-05-29
Deposition Author(s): Lascombe, M.-B., Ponchet, M., Venard, P., Milat, M.-L., Blein, J.-P., Prange, T.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.45 Å
R-Value Free: 0.188
R-Value Work: 0.127
R-Value Observed: 0.127

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

The 1.45 A resolution structure of the cryptogein-cholesterol complex: a close-up view of a sterol carrier protein (SCP) active site.

Lascombe, M.B., Ponchet, M., Venard, P., Milat, M.L., Blein, J.P., Prange, T.

(2002) Acta Crystallogr D Biol Crystallogr 58: 1442-1447

PubMed: 12198300 Search on PubMed
DOI: https://doi.org/10.1107/S0907444902011745
Primary Citation of Related Structures:
1LRI

PubMed Abstract:
Cryptogein is a small 10 kDa elicitor produced by the phytoparasitic oomycete Phytophthora cryptogea. The protein also displays a sterol carrier activity. The native protein crystallizes in space group P4(1)22, with unit-cell parameters a = b = 46.51, c = 134.9 A (diffraction limit: 2.1 A). Its complex with cholesterol crystallizes in space group C222(1), with unit-cell parameters a = 30.96, b = 94.8, c = 65.3 A and a resolution enhanced to 1.45 A. The large inner non-specific hydrophobic cavity is able to accommodate a large variety of 3-beta-hydroxy sterols. Cryptogein probably acts as a sterol shuttle helping the pathogen to grow and complete its life cycle.

Organizational Affiliation

Laboratoire de Cristallographie et RMN Biologiques (UMR-8015, CNRS), Faculté de Pharmacie, 4 Avenue de l'Observatoire, 75270 Paris CEDEX 06, France. lascombe@pharmacie.univ-paris5.fr

Macromolecule Content

Total Structure Weight: 10.75 kDa
Atom Count: 861
Modelled Residue Count: 98
Deposited Residue Count: 98
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-elicitin cryptogein	A	98	Phytophthora cryptogea	Mutation(s): 0
UniProt
Find proteins for P15570 (Phytophthora cryptogea) Explore P15570 Go to UniProtKB: P15570
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P15570
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CLR Query on CLR Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	CHOLESTEROL C₂₇ H₄₆ O HVYWMOMLDIMFJA-DPAQBDIFSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.45 Å
R-Value Free: 0.188
R-Value Work: 0.127
R-Value Observed: 0.127
Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 30.964	α = 90
b = 94.8	β = 90
c = 65.296	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
SHELXL-97	refinement
CCP4	data scaling

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2002-05-29

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2002-05-29
Type: Initial release
Version 1.1: 2008-04-28
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2024-10-30
Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary