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- PDB-1hdk: Charcot-Leyden Crystal Protein - pCMBS Complex -

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Basic information

Entry
Database: PDB / ID: 1hdk
TitleCharcot-Leyden Crystal Protein - pCMBS Complex
ComponentsEOSINOPHIL LYSOPHOSPHOLIPASE
KeywordsSERINE ESTERASE / GALECTIN-10 / EOSINOPHIL LYSOPHOSPHOLIPASE
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 / cysteine-type endopeptidase activity involved in apoptotic process / carbohydrate binding / collagen-containing extracellular matrix / 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
PARA-MERCURY-BENZENESULFONIC ACID / Galectin-10
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.8 Å
AuthorsAckerman, S.J. / Savage, M.P. / Liu, L. / Leonidas, D.D. / Kwatia, M.A. / Swaminathan, G.J. / Acharya, K.R.
Citation
Journal: J.Biol.Chem. / Year: 2002
Title: Charcot-Leyden Crystal Protein (Galectin-10) is not a Dual Function Galectin with Lysophospholipase Activity But Binds a Lysophospholipase Inhibitor in a Novel Structural Fashion.
Authors: Ackerman, S.J. / Liu, L. / Kwatia, M.A. / Savage, M.P. / Leonidas, D.D. / Swaminathan, G.J. / Acharya, K.R.
#1: Journal: Biochemistry / Year: 1999
Title: Selective Recognition of Mannose by Human Eosinophil Charcot-Leyden Crystal Protein (Galectin-10): A Crystallographic Study at 1.8 A Resolution
Authors: Swaminathan, G.J. / Leonidas, D.D. / Savage, M.P. / Ackerman, S.J. / Acharya, K.R.
#2: 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.
History
DepositionNov 16, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 15, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 15, 2015Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Other / Version format compliance
Revision 2.0May 29, 2019Group: Atomic model / Data collection ...Atomic model / Data collection / Experimental preparation / Other
Category: atom_site / diffrn_source ...atom_site / diffrn_source / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _diffrn_source.pdbx_synchrotron_site / _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
Revision 2.1May 8, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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: EOSINOPHIL LYSOPHOSPHOLIPASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,0843
Polymers16,3691
Non-polymers7162
Water1,44180
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)49.547, 49.547, 261.645
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-2071-

HOH

21A-2072-

HOH

DetailsBIOLOGICAL_UNIT: MONOMERA CRYSTAL PACKING DIMERIC ASSEMBLY CAN BE GENERATED USINGTHE SYMMETRY OPERATION -X, Y, 1/2 -Z. THIS CASE OF STRONGCRYSTAL PACKING HAS A DIFFERENCE IN ACCESSIBLE SURFACE AREAPER CHAIN BETWEEN THE ISOLATED CHAIN AND THAT FOR THE CHAININ THE COMPLEX OF 721.9 ANGSTROM**2

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Components

#1: Protein EOSINOPHIL LYSOPHOSPHOLIPASE / CHARCOT-LEYDEN CRYSTAL PROTEIN / GALECTIN-10 / LYSOLECITHIN ACYLHYDROLASE / SERINE ESTERASE


Mass: 16368.690 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: COVALENTLY BOUND TO PCMBS / Source: (natural) HOMO SAPIENS (human) / Cell: EOSINOPHIL / Cellular location: PRIMARY GRANULE / Organelle: GRANULE / Tissue: BLOOD / References: UniProt: Q05315, lysophospholipase
#2: Chemical ChemComp-PMB / PARA-MERCURY-BENZENESULFONIC ACID


Mass: 357.757 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H5HgO3S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 80 / Source method: isolated from a natural source / Formula: H2O
Compound detailsFUNCTION: MAY HAVE BOTH, LYSOPHOSPHOLIPASE AND CARBOHYDRATE- BINDING ACTIVITIES. CATALYTIC ACTIVITY: ...FUNCTION: MAY HAVE BOTH, LYSOPHOSPHOLIPASE AND CARBOHYDRATE- BINDING ACTIVITIES. CATALYTIC ACTIVITY: 2-LYSOPHOSPHATIDIYLCHOLINE + H(2)O = GLYCEROPHOSPHOCHOLINE + A FATTY ACID ANION. SUBCELLULAR LOCATION: LOCALIZED IN GRANULES FROM WHERE IT MAY BE SECRETED OR TRANSPORTED TO OTHER LOCATIONS IN THE CELL. TISSUE SPECIFICITY: EXPRESSED EXCLUSIVELY BY EOSINOPHILS AND BASOPHILS. NOT DETECTED IN MONOCYTES AND NEUTROPHILS. DISEASE: FORMS HEXAGONAL BIPYRAMIDAL CRYSTALS, KNOWN AS CHARCOT- LEYDEN CRYSTALS, IN TISSUES AND SECRETIONS FROM SITES OF EOSINOPHIL-ASSOCIATED INFLAMMATION AND SOME MYELOID LEUKEMIAS. SIMILARITY: BELONGS TO THE GALAPTIN (S-LECTIN) FAMILY.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 2.81 Å3/Da / Density % sol: 55.87 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 7
Details: TRIS-ACETATE PH7.0 100MM HANGING DROP VAPOR DIFFUSION, pH 7.00
Crystal grow
*PLUS
Temperature: 16 ℃ / pH: 10.5 / Method: vapor diffusion, hanging drop
Details: Leonidas, D.D., (1995) Structure (London), 3, 1379.
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: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X31 / Wavelength: 0.92
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 15, 1996 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 1.8→20 Å / Num. obs: 16423 / % possible obs: 87.8 % / Observed criterion σ(I): 0 / Redundancy: 1.5 % / Biso Wilson estimate: 17.9 Å2 / Rmerge(I) obs: 0.079 / Net I/σ(I): 12.7
Reflection shellResolution: 1.8→1.87 Å / Redundancy: 1.4 % / Rmerge(I) obs: 0.127 / Mean I/σ(I) obs: 3.4 / % possible all: 72.4
Reflection
*PLUS
Lowest resolution: 99 Å / Num. obs: 16447 / % possible obs: 87.7 % / Num. measured all: 105494

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Processing

Software
NameVersionClassification
X-PLOR3.851refinement
DENZOdata reduction
SCALEPACKdata scaling
PHASESphasing
RefinementMethod to determine structure: MIR / Resolution: 1.8→20 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Details: BULK SOLVENT MODEL USED THE LAST TWO RESIDUES WERE NOT VISIBLE IN THE ELECTRON DENSITY MAPS
RfactorNum. reflection% reflectionSelection details
Rfree0.221 797 4.9 %RANDOM
Rwork0.199 ---
obs0.199 16423 87.4 %-
Displacement parametersBiso mean: 21 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.25 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.22 Å0.21 Å
Refinement stepCycle: LAST / Resolution: 1.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1131 0 22 80 1233
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.008
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_d29.5
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.67
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.331.5
X-RAY DIFFRACTIONx_mcangle_it2.232
X-RAY DIFFRACTIONx_scbond_it3.062
X-RAY DIFFRACTIONx_scangle_it4.42.5
LS refinement shellResolution: 1.8→1.91 Å / Rfactor Rfree error: 0.03 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.303 99 4.7 %
Rwork0.291 2012 -
obs--69.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REPTOPHCSDX.PR
X-RAY DIFFRACTION2PARTOP
X-RAY DIFFRACTION3LIGLIG
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_deg29.5
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.67

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