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- PDB-1g86: CHARCOT-LEYDEN CRYSTAL PROTEIN/N-ETHYLMALEIMIDE COMPLEX -

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Basic information

Entry
Database: PDB / ID: 1g86
TitleCHARCOT-LEYDEN CRYSTAL PROTEIN/N-ETHYLMALEIMIDE COMPLEX
ComponentsCHARCOT-LEYDEN CRYSTAL PROTEIN
KeywordsHYDROLASE / beta barrel
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
N-ETHYLMALEIMIDE / Galectin-10
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsAckerman, S.J. / Liu, L. / Kwatia, M.A. / Savage, M.P. / Leonidas, D.D. / 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: RCSB / Processing site: RCSB
Revision 1.0Jun 19, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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: CHARCOT-LEYDEN CRYSTAL PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,7503
Polymers16,5001
Non-polymers2502
Water1,47782
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.710, 49.710, 264.860
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-171-

HOH

21A-173-

HOH

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Components

#1: Protein CHARCOT-LEYDEN CRYSTAL PROTEIN / EOSINOPHIL LYSOPHOSPHOLIPASE


Mass: 16499.887 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: EOSINOPHIL PRIMARY GRANULE / Source: (natural) Homo sapiens (human) / References: UniProt: Q05315, lysophospholipase
#2: Chemical ChemComp-NEQ / N-ETHYLMALEIMIDE


Mass: 125.125 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H7NO2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 82 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.86 Å3/Da / Density % sol: 57.01 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: Tris-Acetate 0.1M, pH7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
12931
22931
Diffraction source
SourceSiteBeamlineTypeIDWavelength
SYNCHROTRONSRS PX9.610.87
ROTATING ANODERIGAKU RU30021.5416
Detector
TypeIDDetectorDateDetails
MARRESEARCH1IMAGE PLATEOct 1, 1994Mirrors
MARRESEARCH2IMAGE PLATEOct 1, 1995Mirrors
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1MADMx-ray1
2SINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
10.871
21.54161
ReflectionResolution: 1.8→20 Å / Num. all: 17870 / Num. obs: 17573 / % possible obs: 93.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.08 % / Biso Wilson estimate: 15.5 Å2 / Rmerge(I) obs: 0.132 / Rsym value: 0.053 / Net I/σ(I): 12.8
Reflection shellResolution: 1.8→1.91 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.233 / Mean I/σ(I) obs: 7.2 / Num. unique all: 2832 / Rsym value: 0.182 / % possible all: 91.6

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Processing

Software
NameVersionClassification
X-PLORmodel building
X-PLOR3.851refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1LCL

1lcl


Resolution: 1.8→20 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.242 855 4.8 %RANDOM
Rwork0.203 ---
obs0.203 17573 93.3 %-
all-17870 --
Displacement parametersBiso mean: 24.1 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.22 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.18 Å0.2 Å
Refinement stepCycle: LAST / Resolution: 1.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1145 0 18 82 1245
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_angle_deg1.6
X-RAY DIFFRACTIONx_dihedral_angle_d29
X-RAY DIFFRACTIONx_improper_angle_d0.81
X-RAY DIFFRACTIONx_mcbond_it1.611.5
X-RAY DIFFRACTIONx_mcangle_it2.592
X-RAY DIFFRACTIONx_scbond_it3.452
X-RAY DIFFRACTIONx_scangle_it5.322.5
LS refinement shellResolution: 1.8→1.91 Å / Rfactor Rfree error: 0.029 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.333 129 4.5 %
Rwork0.289 2713 -
obs-2832 92 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramtophcsdx.pro
X-RAY DIFFRACTION2param.watertopow.water
X-RAY DIFFRACTION3nem.parnem.top

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