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- PDB-1lri: BETA-CRYPTOGEIN-CHOLESTEROL COMPLEX -

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Basic information

Entry
Database: PDB / ID: 1lri
TitleBETA-CRYPTOGEIN-CHOLESTEROL COMPLEX
ComponentsBeta-elicitin cryptogein
KeywordsTOXIN / cryptogein / cholesterol / sterol carrier protein
Function / homology
Function and homology information


symbiont-mediated perturbation of host 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
CHOLESTEROL / Beta-elicitin cryptogein
Similarity search - Component
Biological speciesPhytophthora cryptogea (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.45 Å
AuthorsLascombe, M.-B. / Ponchet, M. / Venard, P. / Milat, M.-L. / Blein, J.-P. / Prange, T.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2002
Title: The 1.45 A resolution structure of the cryptogein-cholesterol complex: a close-up view of a sterol carrier protein (SCP) active site.
Authors: Lascombe, M.B. / Ponchet, M. / Venard, P. / Milat, M.L. / Blein, J.P. / Prange, T.
History
DepositionMay 15, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 29, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_initial_refinement_model / pdbx_modification_feature / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Beta-elicitin cryptogein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,7493
Polymers10,3271
Non-polymers4222
Water1,78399
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)30.964, 94.800, 65.296
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-100-

CL

21A-185-

HOH

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Components

#1: Protein Beta-elicitin cryptogein / fungal elicitor cryptogein / CRY


Mass: 10326.790 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Phytophthora cryptogea (eukaryote) / References: UniProt: P15570
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-CLR / CHOLESTEROL


Mass: 386.654 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H46O
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 99 / 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: 1.92 Å3/Da / Density % sol: 46.96 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: sodium chloride, cholesterol, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Crystal grow
*PLUS
Components of the solutions
*PLUS
Conc.: 4.5 M / Chemical formula: NaCl

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: SYNCHROTRON / Site: LURE / Beamline: DW32 / Wavelength: 0.964 / Wavelength: 0.964 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Dec 17, 2001 / Details: FOCUSING MIRRORS
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.964 Å / Relative weight: 1
ReflectionResolution: 1.45→9.6 Å / Num. obs: 17432 / % possible obs: 99.1 % / Observed criterion σ(F): 4 / Observed criterion σ(I): 6 / Redundancy: 3.9 % / Biso Wilson estimate: 18.4 Å2 / Rmerge(I) obs: 0.39 / Rsym value: 0.41 / Net I/σ(I): 16.5
Reflection shellResolution: 1.448→1.48 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.152 / Mean I/σ(I) obs: 4.1 / Num. unique all: 1084 / Rsym value: 0.144 / % possible all: 97.3
Reflection
*PLUS
Lowest resolution: 10 Å / Num. measured all: 64233
Reflection shell
*PLUS
% possible obs: 96 % / Rmerge(I) obs: 0.213 / Mean I/σ(I) obs: 4.6

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
SHELXL-97refinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 1BXM

1bxm


Resolution: 1.45→9.6 Å / Num. parameters: 7573 / Num. restraintsaints: 9191 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: FULL ANISOTROPIC REFINEMENT EXCEPT IN DiSORDERED RESIDUES
RfactorNum. reflection% reflectionSelection details
Rfree0.1881 1089 6.2 %RANDOM
Rwork0.127 ---
all0.13 17432 --
obs0.127 16165 97.9 %-
Solvent computationSolvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-228
Displacement parametersBiso mean: 19.5 Å2
Refine analyzeNum. disordered residues: 4 / Occupancy sum hydrogen: 747.23 / Occupancy sum non hydrogen: 841.24
Refinement stepCycle: LAST / Resolution: 1.45→9.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms733 0 29 99 861
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.012
X-RAY DIFFRACTIONs_angle_d0.029
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0228
X-RAY DIFFRACTIONs_zero_chiral_vol0.058
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.059
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.022
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.008
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.056
X-RAY DIFFRACTIONs_approx_iso_adps0.078
LS refinement shell
Resolution (Å)Rfactor RfreeRfactor RworkRefine-IDNum. reflection obs% reflection obs (%)
1.45-1.530.1690.119X-RAY DIFFRACTION261098.9
1.53-1.660.1630.109X-RAY DIFFRACTION3175100
1.66-1.890.160.102X-RAY DIFFRACTION3718100
1.89-2.30.1570.102X-RAY DIFFRACTION3507100
2.3-3.20.180.124X-RAY DIFFRACTION2802100
3.2-100.240.17X-RAY DIFFRACTION162096.6
Software
*PLUS
Name: SHELXL / Version: 97 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 10 Å / Num. reflection Rfree: 992 / % reflection Rfree: 8 % / Rfactor all: 0.13 / Rfactor Rfree: 0.168
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_angle_d0.03
X-RAY DIFFRACTIONs_plane_restr0.03

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