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- PDB-4wka: Crystal structure of human chitotriosidase-1 catalytic domain at ... -

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Basic information

Entry
Database: PDB / ID: 4wka
TitleCrystal structure of human chitotriosidase-1 catalytic domain at 0.95 A resolution
ComponentsChitotriosidase-1
KeywordsHYDROLASE / CHIT1 / GH18 chitinase / protonation states / hydrolysis / catalytic mechanism
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 / Glycosyl hydrolases family 18 (GH18) domain profile. / 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
L(+)-TARTARIC ACID / Chitotriosidase-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.95 Å
AuthorsFadel, F. / Zhao, Y. / Cachau, R. / Cousido-Siah, A. / Ruiz, F.X. / Harlos, K. / Howard, E. / Mitschler, A. / Podjarny, A.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2015
Title: New insights into the enzymatic mechanism of human chitotriosidase (CHIT1) catalytic domain by atomic resolution X-ray diffraction and hybrid QM/MM.
Authors: Fadel, F. / Zhao, Y. / Cachau, R. / Cousido-Siah, A. / Ruiz, F.X. / Harlos, K. / Howard, E. / Mitschler, A. / Podjarny, A.
History
DepositionOct 2, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jul 8, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 15, 2015Group: Database references
Revision 1.2Jul 22, 2015Group: Database references
Revision 1.3Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Nov 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-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,5243
Polymers42,2241
Non-polymers3002
Water10,215567
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area390 Å2
ΔGint1 kcal/mol
Surface area15210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.327, 103.701, 41.688
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Chitotriosidase-1 / Chitinase-1


Mass: 42224.289 Da / Num. of mol.: 1 / Fragment: UNP residues 22-386
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CHIT1 / Cell line (production host): HEK293T / Production host: Homo sapiens (human) / References: UniProt: Q13231, chitinase
#2: Chemical ChemComp-TLA / L(+)-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H6O6
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 567 / 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

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Sample preparation

CrystalDensity Matthews: 2.18 Å3/Da / Density % sol: 43.68 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop
Details: 23 % (w/v) polyethylene glycol (PEG) 3350, 0.2 M potassium sodium tartrate (PST) at pH 7.2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.8 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 3, 2014
RadiationMonochromator: Bartels Monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8 Å / Relative weight: 1
ReflectionResolution: 0.95→50 Å / Num. obs: 223038 / % possible obs: 95.99 % / Redundancy: 12.6 % / Rsym value: 0.059 / Net I/σ(I): 36.08
Reflection shellResolution: 0.95→0.98 Å / Redundancy: 9.9 % / Rmerge(I) obs: 0.766 / Mean I/σ(I) obs: 2.57 / % possible all: 82.51

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: dev_1702)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1GUV

1guv


Resolution: 0.95→42.663 Å / SU ML: 0.07 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 9.51 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1227 11188 5.02 %Random 5%
Rwork0.1123 ---
obs0.1129 223022 95.98 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 0.95→42.663 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2909 0 20 567 3496
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073591
X-RAY DIFFRACTIONf_angle_d1.3234926
X-RAY DIFFRACTIONf_dihedral_angle_d14.6331343
X-RAY DIFFRACTIONf_chiral_restr0.081501
X-RAY DIFFRACTIONf_plane_restr0.007672
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
0.9502-0.9610.23332770.23965586X-RAY DIFFRACTION77
0.961-0.97230.20892850.20986075X-RAY DIFFRACTION83
0.9723-0.98410.1883410.19276360X-RAY DIFFRACTION88
0.9841-0.99660.18033420.17576660X-RAY DIFFRACTION91
0.9966-1.00970.15973490.1596808X-RAY DIFFRACTION93
1.0097-1.02350.16033490.13986953X-RAY DIFFRACTION95
1.0235-1.03820.14143660.1226982X-RAY DIFFRACTION96
1.0382-1.05360.12363540.11137056X-RAY DIFFRACTION97
1.0536-1.07010.11733490.10547033X-RAY DIFFRACTION96
1.0701-1.08770.11893710.09727086X-RAY DIFFRACTION97
1.0877-1.10640.10474220.09257038X-RAY DIFFRACTION97
1.1064-1.12650.11063770.09137129X-RAY DIFFRACTION97
1.1265-1.14820.10123470.08887080X-RAY DIFFRACTION97
1.1482-1.17160.10083990.08517110X-RAY DIFFRACTION97
1.1716-1.19710.09643630.08637145X-RAY DIFFRACTION98
1.1971-1.2250.09744110.08527102X-RAY DIFFRACTION97
1.225-1.25560.1073880.08637198X-RAY DIFFRACTION98
1.2556-1.28960.10783540.0887191X-RAY DIFFRACTION98
1.2896-1.32750.1023960.08767220X-RAY DIFFRACTION98
1.3275-1.37040.10294160.08887185X-RAY DIFFRACTION98
1.3704-1.41930.10793710.08987278X-RAY DIFFRACTION99
1.4193-1.47620.09723810.09357261X-RAY DIFFRACTION99
1.4762-1.54340.11824080.09287259X-RAY DIFFRACTION98
1.5434-1.62470.10593890.09577281X-RAY DIFFRACTION99
1.6247-1.72650.124020.10127367X-RAY DIFFRACTION99
1.7265-1.85980.11713920.10727358X-RAY DIFFRACTION99
1.8598-2.0470.11633650.11017422X-RAY DIFFRACTION100
2.047-2.34320.12214100.11137461X-RAY DIFFRACTION100
2.3432-2.95210.13334010.12777537X-RAY DIFFRACTION100
2.9521-42.70660.13914130.13557613X-RAY DIFFRACTION97

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