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- PDB-5hbf: Crystal structure of human full-length chitotriosidase (CHIT1) -

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Basic information

Entry
Database: PDB / ID: 5hbf
TitleCrystal structure of human full-length chitotriosidase (CHIT1)
ComponentsChitotriosidase-1
KeywordsHYDROLASE / chitotriosidase / chitin binding domain / CBM14 / seeding
Function / homology
Function and homology information


endochitinase activity / polysaccharide digestion / Digestion of dietary carbohydrate / chitinase / chitinase activity / chitin catabolic process / chitin binding / polysaccharide catabolic process / hydrolase activity, hydrolyzing O-glycosyl compounds / response to bacterium ...endochitinase activity / polysaccharide digestion / Digestion of dietary carbohydrate / chitinase / chitinase activity / 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 / Chitinase II ...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. / Glycoside hydrolase family 18, catalytic domain / Glycosyl hydrolases family 18 / Chitinase A; domain 3 / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Roll / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsFadel, F. / Zhao, Y. / Cousido-Siah, A. / Ruiz, F.X. / Mitschler, A. / Podjarny, A.
CitationJournal: Plos One / Year: 2016
Title: X-Ray Crystal Structure of the Full Length Human Chitotriosidase (CHIT1) Reveals Features of Its Chitin Binding Domain.
Authors: Fadel, F. / Zhao, Y. / Cousido-Siah, A. / Ruiz, F.X. / Mitschler, A. / Podjarny, A.
History
DepositionDec 31, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 4, 2016Provider: repository / Type: Initial release
Revision 1.1May 11, 2016Group: Database references
Revision 1.2Sep 27, 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 / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Chitotriosidase-1
B: Chitotriosidase-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,1926
Polymers106,8242
Non-polymers3684
Water3,153175
1
A: Chitotriosidase-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,5963
Polymers53,4121
Non-polymers1842
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Chitotriosidase-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,5963
Polymers53,4121
Non-polymers1842
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3190 Å2
ΔGint-14 kcal/mol
Surface area36630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.143, 106.661, 85.670
Angle α, β, γ (deg.)90.00, 107.13, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Chitotriosidase-1 / Chitinase-1


Mass: 53411.945 Da / Num. of mol.: 2
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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 175 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.09 Å3/Da / Density % sol: 41.16 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: 15% PEG3350, 0.02 M HEPES, pH 6.8, 0.2% MPD, 0.2% 1,2,3-heptanetriol, 0.2% diethylenetriaminepentakis, 0.2% D-sorbitol, 0.2% glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Mar 31, 2014
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.95→44.69 Å / Num. obs: 114875 / % possible obs: 96.63 % / Redundancy: 3.9 % / Rsym value: 0.057 / Net I/σ(I): 15.06
Reflection shellResolution: 1.95→2.013 Å / Redundancy: 3.9 % / Mean I/σ(I) obs: 1.85 / Rsym value: 0.63 / % possible all: 89.4

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Processing

Software
NameVersionClassification
PHENIXdev_1255refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4WJX

4wjx


Resolution: 1.95→44.686 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 30.65 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2454 3655 3.18 %RANDOM
Rwork0.2051 ---
obs0.2064 114846 90.15 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.95→44.686 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6675 0 24 175 6874
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076956
X-RAY DIFFRACTIONf_angle_d1.0959412
X-RAY DIFFRACTIONf_dihedral_angle_d15.262510
X-RAY DIFFRACTIONf_chiral_restr0.077981
X-RAY DIFFRACTIONf_plane_restr0.0051233
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9435-1.96910.44541070.39563352X-RAY DIFFRACTION70
1.9691-1.99610.38831360.35324314X-RAY DIFFRACTION92
1.9961-2.02460.39021460.334405X-RAY DIFFRACTION93
2.0246-2.05480.36641450.30464474X-RAY DIFFRACTION93
2.0548-2.08690.3241380.28994402X-RAY DIFFRACTION93
2.0869-2.12110.30311400.28284437X-RAY DIFFRACTION93
2.1211-2.15770.29921450.27664313X-RAY DIFFRACTION92
2.1577-2.19690.31131350.274420X-RAY DIFFRACTION92
2.1969-2.23920.33661410.26444410X-RAY DIFFRACTION92
2.2392-2.28490.36161450.25624269X-RAY DIFFRACTION91
2.2849-2.33460.31171450.2594307X-RAY DIFFRACTION91
2.3346-2.38890.34741440.25814241X-RAY DIFFRACTION90
2.3889-2.44860.32271450.24784227X-RAY DIFFRACTION88
2.4486-2.51480.28341260.23143971X-RAY DIFFRACTION84
2.5148-2.58880.251330.21964079X-RAY DIFFRACTION86
2.5888-2.67240.29751360.22424183X-RAY DIFFRACTION88
2.6724-2.76790.25181440.21454286X-RAY DIFFRACTION90
2.7679-2.87870.25251470.21664513X-RAY DIFFRACTION95
2.8787-3.00960.31111460.20854463X-RAY DIFFRACTION95
3.0096-3.16830.25761500.20694502X-RAY DIFFRACTION94
3.1683-3.36670.24291410.19584428X-RAY DIFFRACTION94
3.3667-3.62660.21151480.17514367X-RAY DIFFRACTION92
3.6266-3.99130.20131440.16614270X-RAY DIFFRACTION90
3.9913-4.56840.17331380.15134055X-RAY DIFFRACTION85
4.5684-5.75370.19211350.15013989X-RAY DIFFRACTION84
5.7537-44.69770.1611550.15914514X-RAY DIFFRACTION95

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