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- PDB-1lg2: CRYSTAL STRUCTURE OF HUMAN CHITOTRIOSIDASE IN COMPLEX WITH ETHYLE... -

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Basic information

Entry
Database: PDB / ID: 1lg2
TitleCRYSTAL STRUCTURE OF HUMAN CHITOTRIOSIDASE IN COMPLEX WITH ETHYLENE GLYCOL
Componentschitotriosidase
KeywordsHYDROLASE / CHITINASE / CHITIN / GAUCHER
Function / homology
Function and homology information


polysaccharide digestion / Digestion of dietary carbohydrate / chitinase activity / endochitinase activity / chitinase / chitin catabolic process / chitin binding / polysaccharide catabolic process / hydrolase activity, hydrolyzing O-glycosyl compounds / response to bacterium ...polysaccharide digestion / Digestion of dietary carbohydrate / chitinase activity / endochitinase activity / chitinase / chitin catabolic process / chitin binding / polysaccharide catabolic process / hydrolase activity, hydrolyzing O-glycosyl compounds / response to bacterium / specific granule lumen / tertiary granule lumen / lysosome / immune response / Neutrophil degranulation / extracellular space / extracellular region
Similarity search - Function
Chitin-binding domain type 2 / Chitin binding domain / Chitin binding Peritrophin-A domain / Chitin-binding type-2 domain profile. / Chitin binding domain superfamily / Chitinase A; domain 3 - #10 / Glycosyl hydrolases family 18 (GH18) active site / Glycosyl hydrolases family 18 (GH18) active site signature. / : / Chitinase insertion domain superfamily ...Chitin-binding domain type 2 / Chitin binding domain / Chitin binding Peritrophin-A domain / Chitin-binding type-2 domain profile. / Chitin binding domain superfamily / Chitinase A; domain 3 - #10 / Glycosyl hydrolases family 18 (GH18) active site / Glycosyl hydrolases family 18 (GH18) active site signature. / : / Chitinase insertion domain superfamily / Chitinase II / Glyco_18 / Glycosyl hydrolases family 18 (GH18) domain profile. / Glycosyl hydrolases family 18 / Glycoside hydrolase family 18, catalytic domain / Chitinase A; domain 3 / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Roll / Alpha Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsFusetti, F. / Rozeboom, H.J. / Dijkstra, B.W.
CitationJournal: J.Biol.Chem. / Year: 2002
Title: Structure of Human Chitotriosidase. Implications for Specific Inhibitor Design and Function of Mammalian Chitinase-Like Lectins.
Authors: Fusetti, F. / Von Moeller, H. / Houston, D. / Rozeboom, H.J. / Dijkstra, B.W. / Boot, R.G. / Aerts, J.M. / Van Aalten, D.M.
History
DepositionApr 14, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 18, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 20, 2012Group: Data collection
Revision 1.4Apr 3, 2024Group: 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
Revision 1.5Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: chitotriosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,0956
Polymers40,7851
Non-polymers3105
Water3,621201
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.173, 47.285, 84.726
Angle α, β, γ (deg.)90.00, 102.58, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein chitotriosidase


Mass: 40784.695 Da / Num. of mol.: 1 / Fragment: residues 22-386
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): BHK / Production host: Mesocricetus auratus (golden hamster) / References: UniProt: Q13231
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 201 / 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: 2.26 Å3/Da / Density % sol: 45.2 %
Crystal growpH: 5.6 / Details: pH 5.6
Crystal grow
*PLUS
pH: 8.7 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
150 mMTris-HCl1droppH8.7
27.7 mg/mlprotein1drop
30.1 MTris-HCl1reservoirpH8.5
430 %PEG40001reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Wavelength: 1.5418
DetectorType: MAC Science DIP-2030 / Detector: IMAGE PLATE / Date: Jul 1, 2001
RadiationMonochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 20542 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 3.5 % / Biso Wilson estimate: 22.184 Å2 / Rmerge(I) obs: 0.072 / Net I/σ(I): 18.9
Reflection shellResolution: 2.1→2.15 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.225 / Mean I/σ(I) obs: 5.9 / Num. unique all: 1330 / % possible all: 97
Reflection
*PLUS
Highest resolution: 2.1 Å / Lowest resolution: 13.4 Å / Num. obs: 20533 / Redundancy: 3.6 % / Num. measured all: 73055
Reflection shell
*PLUS
% possible obs: 97 % / Redundancy: 3.2 % / Num. unique obs: 1330 / Num. measured obs: 4290 / Mean I/σ(I) obs: 4.6

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: HUMAN CHITOTRIOSIADSE TETRAGONAL CRYSTAL FORM

Resolution: 2.1→23.64 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 1089189.58 / Data cutoff high rms absF: 1089189.58 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.228 2077 10.1 %RANDOM
Rwork0.19 ---
obs0.19 20524 99.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 52.1673 Å2 / ksol: 0.395364 e/Å3
Displacement parametersBiso mean: 19.6 Å2
Baniso -1Baniso -2Baniso -3
1--0.7 Å20 Å2-0.28 Å2
2---2.03 Å20 Å2
3---2.73 Å2
Refine analyzeLuzzati coordinate error free: 0.26 Å / Luzzati sigma a free: 0.13 Å
Refinement stepCycle: LAST / Resolution: 2.1→23.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2797 0 20 201 3018
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
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_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.3
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.75
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.141.5
X-RAY DIFFRACTIONc_mcangle_it1.642
X-RAY DIFFRACTIONc_scbond_it2.032
X-RAY DIFFRACTIONc_scangle_it2.862.5
LS refinement shellResolution: 2.1→2.23 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.234 336 10.1 %
Rwork0.191 2989 -
obs--97.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAM&_1_TOPOLOGY_INFILE_1
X-RAY DIFFRACTION2CHITO_CIS_PEPTIDE.PARAM&_1_TOPOLOGY_INFILE_2
X-RAY DIFFRACTION3CARBOHYDRATE.PARAM&_1_TOPOLOGY_INFILE_3
X-RAY DIFFRACTION4WATER_REP.PARAM&_1_TOPOLOGY_INFILE_4
X-RAY DIFFRACTION5EG.PARAM&_1_TOPOLOGY_INFILE_5
Refinement
*PLUS
Highest resolution: 2.1 Å / Lowest resolution: 13.4 Å / Rfactor Rfree: 0.227 / Rfactor Rwork: 0.204
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.3
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.75

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