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- PDB-1lcl: CHARCOT-LEYDEN CRYSTAL PROTEIN -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 1lcl
TitleCHARCOT-LEYDEN CRYSTAL PROTEIN
ComponentsLYSOPHOSPHOLIPASE
KeywordsSERINE ESTERASE / CHARCOT-LEYDEN CRYSTAL PROTEIN
Function / homology
Function and homology information


regulation of activated T cell proliferation / regulation of T cell cytokine production / T cell apoptotic process / regulation of T cell anergy / : / carbohydrate binding / identical protein binding / cytosol
Similarity search - Function
Galectin-like / Galactoside-binding lectin / Galectin / Galectin, carbohydrate recognition domain / Galactoside-binding lectin / Galactoside-binding lectin (galectin) domain profile. / Jelly Rolls - #200 / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.8 Å
AuthorsAcharya, K.R. / Leonidas, D.D.
Citation
Journal: Structure / Year: 1995
Title: Crystal structure of human Charcot-Leyden crystal protein, an eosinophil lysophospholipase, identifies it as a new member of the carbohydrate-binding family of galectins.
Authors: Leonidas, D.D. / Elbert, B.L. / Zhou, Z. / Leffler, H. / Ackerman, S.J. / Acharya, K.R.
#1: Journal: J.Immunol. / Year: 1993
Title: Molecular Cloning and Characterization of Human Eosinophil Charcot-Leyden Crystal Protein (Lysophospholipase). Similarities to Ige Binding Proteins and the S-Type Animal Lectin Superfamily
Authors: Ackerman, S.J. / Corrette, S.E. / Rosenberg, H.F. / Bennett, J.C. / Mastrianni, D.M. / Nicholson-Weller, A. / Weller, P.F. / Chin, D.T. / Tenen, D.G.
History
DepositionJan 18, 1996Processing site: BNL
Revision 1.0Jan 11, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: LYSOPHOSPHOLIPASE


Theoretical massNumber of molelcules
Total (without water)16,5001
Polymers16,5001
Non-polymers00
Water1,38777
1
A: LYSOPHOSPHOLIPASE

A: LYSOPHOSPHOLIPASE


Theoretical massNumber of molelcules
Total (without water)33,0002
Polymers33,0002
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_555-x+y,y,-z+1/21
Unit cell
Length a, b, c (Å)49.600, 49.600, 262.200
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-189-

HOH

21A-190-

HOH

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Components

#1: Protein LYSOPHOSPHOLIPASE / CHARCOT-LEYDEN CRYSTAL PROTEIN


Mass: 16499.887 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell: EOSINOPHIL / References: UniProt: Q05315, lysophospholipase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 77 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.82 Å3/Da / Density % sol: 52 %
Crystal growpH: 7 / Details: pH 7.0
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 16 ℃ / pH: 10.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
15 mg/mlprotein1drop
20.1 MTris1drop
30.2 MTris-acetate1reservoir

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Data collection

DiffractionMean temperature: 289 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 1 / Wavelength: 0.8, 1.0
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: 1994
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
111
20.81
ReflectionResolution: 1.8→40 Å / Num. obs: 18046 / % possible obs: 94.4 % / Observed criterion σ(I): -3 / Redundancy: 5.3 % / Rmerge(I) obs: 0.077
Reflection
*PLUS
Num. measured all: 75363

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.1phasing
RefinementResolution: 1.8→8 Å / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.258 -5 %
Rwork0.2 --
obs0.2 17687 95 %
Displacement parametersBiso mean: 20.7 Å2
Refine analyzeLuzzati coordinate error obs: 0.2 Å
Refinement stepCycle: LAST / Resolution: 1.8→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1145 0 0 77 1222
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.01
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_deg1.61
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d27.96
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.3
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.5
X-RAY DIFFRACTIONx_mcangle_it2
X-RAY DIFFRACTIONx_scbond_it1.5
X-RAY DIFFRACTIONx_scangle_it2
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.2 / Rfactor Rwork: 0.2
Solvent computation
*PLUS
Displacement parameters
*PLUS

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