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- PDB-1qkq: CHARCOT-LEYDEN CRYSTAL PROTEIN - MANNOSE COMPLEX -

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Basic information

Entry
Database: PDB / ID: 1qkq
TitleCHARCOT-LEYDEN CRYSTAL PROTEIN - MANNOSE COMPLEX
ComponentsEOSINOPHIL LYSOPHOSPHOLIPASE
KeywordsHYDROLASE / SERINE ESTERASE
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 / 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
alpha-D-mannopyranose / Galectin-10
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsSwaminathan, G.J. / Leonidas, D.D. / Acharya, K.R.
Citation
Journal: Biochemistry / Year: 1999
Title: Selective recognition of mannose by the 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.
#1: 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
DepositionJul 31, 1999Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 18, 2000Provider: repository / Type: Initial release
Revision 1.1Aug 29, 2012Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Other / Refinement description / Structure summary / Version format compliance
Revision 1.2Sep 18, 2019Group: Data collection / Database references / Category: citation / reflns
Item: _citation.page_last / _citation.pdbx_database_id_DOI ..._citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _reflns.pdbx_Rsym_value
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)16,6802
Polymers16,5001
Non-polymers1801
Water1,31573
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)49.600, 49.600, 263.130
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-2064-

HOH

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Components

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


Mass: 16499.887 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) HOMO SAPIENS (human) / Cell: EOSINOPHIL / Cellular location: PRIMARY GRANULE / References: UniProt: Q05315, lysophospholipase
#2: Sugar ChemComp-MAN / alpha-D-mannopyranose / alpha-D-mannose / D-mannose / mannose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DManpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-mannopyranoseCOMMON NAMEGMML 1.0
a-D-ManpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
ManSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 73 / 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: 2.83 Å3/Da / Density % sol: 52 %
Crystal growpH: 7 / Details: 02M TRIS.HCL PH 7.0
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 MTris-HCl1drop
30.2 MTris-acetate1reservoir

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.876
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 15, 1997 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.876 Å / Relative weight: 1
ReflectionResolution: 1.8→40 Å / Num. obs: 18942 / % possible obs: 99.3 % / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Biso Wilson estimate: 16.3 Å2 / Rsym value: 0.074 / Net I/σ(I): 7.8
Reflection shellResolution: 1.8→1.91 Å / Redundancy: 2.1 % / % possible all: 98.7
Reflection
*PLUS
Num. measured all: 138775 / Rmerge(I) obs: 0.074
Reflection shell
*PLUS
% possible obs: 98.7 %

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Processing

Software
NameVersionClassification
CNS0.5refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1LCL

1lcl


Resolution: 1.8→40 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 1856505.66 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Details: BULK SOLVENT MODEL USED SIDE CHAIN ELECTRON DENSITY WAS NOT SEEN FOR C-TERMNINAL ARGININE
RfactorNum. reflection% reflectionSelection details
Rfree0.251 901 4.8 %RANDOM
Rwork0.236 ---
obs0.236 18866 99.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 41.4225 Å2 / ksol: 0.349192 e/Å3
Displacement parametersBiso mean: 27.9 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.28 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.16 Å0.23 Å
Refinement stepCycle: LAST / Resolution: 1.8→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1145 0 12 73 1230
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d29.6
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.64
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it2.891.5
X-RAY DIFFRACTIONc_mcangle_it3.482
X-RAY DIFFRACTIONc_scbond_it4.352
X-RAY DIFFRACTIONc_scangle_it5.882.5
LS refinement shellResolution: 1.8→1.91 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.28 159 5.3 %
Rwork0.325 2865 -
obs--98.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2PARAM3.CHOTOPH3.CHO
X-RAY DIFFRACTION3PARAM.WATERTOPOW.WATER
Software
*PLUS
Name: CNS / Version: 0.5 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg29.6
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.64

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