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- PDB-4wkh: Crystal structure of human chitotriosidase-1 catalytic domain in ... -

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Basic information

Entry
Database: PDB / ID: 4wkh
TitleCrystal structure of human chitotriosidase-1 catalytic domain in complex with chitobiose (1mM) at 1.05 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
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.05 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 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.type
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Jan 10, 2024Group: 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
Revision 2.2Oct 23, 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)42,6492
Polymers42,2241
Non-polymers4241
Water9,116506
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area810 Å2
ΔGint-5 kcal/mol
Surface area14880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.500, 105.528, 41.475
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
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: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 506 / 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: 2.22 Å3/Da / Density % sol: 44.49 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop
Details: 25 % (w/v) polyethylene glycol (PEG) 3350, 0.2 M potassium sodium tartrate at pH 7.2, 0.3mM 4-methylumbelliferyl triacetylchitotrioside

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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: Nov 13, 2013
RadiationMonochromator: Bartels Monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8 Å / Relative weight: 1
ReflectionResolution: 1.05→50 Å / Num. obs: 175071 / % possible obs: 99.78 % / Redundancy: 6.2 % / Rsym value: 0.046 / Net I/σ(I): 31.92
Reflection shellResolution: 1.05→1.09 Å / Redundancy: 5 % / Rmerge(I) obs: 0.681 / Mean I/σ(I) obs: 2.24 / % possible all: 98.46

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: dev_1255)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1GUV

1guv


Resolution: 1.05→15.809 Å / SU ML: 0.07 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 12.72 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1534 8758 5 %Random 5%
Rwork0.1434 ---
obs0.1439 175062 99.78 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.05→15.809 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2909 0 29 506 3444
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063374
X-RAY DIFFRACTIONf_angle_d1.2834625
X-RAY DIFFRACTIONf_dihedral_angle_d14.5521283
X-RAY DIFFRACTIONf_chiral_restr0.09491
X-RAY DIFFRACTIONf_plane_restr0.006608
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.0495-1.06140.23832730.2385352X-RAY DIFFRACTION97
1.0614-1.07390.23962860.21785446X-RAY DIFFRACTION99
1.0739-1.0870.21522980.20845460X-RAY DIFFRACTION99
1.087-1.10080.20043200.17765428X-RAY DIFFRACTION100
1.1008-1.11530.18472930.15395488X-RAY DIFFRACTION100
1.1153-1.13050.16942880.1515494X-RAY DIFFRACTION100
1.1305-1.14670.16882980.14435517X-RAY DIFFRACTION100
1.1467-1.16380.14492960.13155452X-RAY DIFFRACTION100
1.1638-1.1820.13672710.12445550X-RAY DIFFRACTION100
1.182-1.20130.1562800.12385500X-RAY DIFFRACTION100
1.2013-1.2220.13822890.12155526X-RAY DIFFRACTION100
1.222-1.24430.12423010.11825498X-RAY DIFFRACTION100
1.2443-1.26820.13832900.11265515X-RAY DIFFRACTION100
1.2682-1.29410.12663020.11355525X-RAY DIFFRACTION100
1.2941-1.32220.1372780.11155507X-RAY DIFFRACTION100
1.3222-1.35290.12583110.10955514X-RAY DIFFRACTION100
1.3529-1.38670.1352600.1135583X-RAY DIFFRACTION100
1.3867-1.42420.12952710.11545549X-RAY DIFFRACTION100
1.4242-1.46610.12652920.1095529X-RAY DIFFRACTION100
1.4661-1.51340.13642820.10735534X-RAY DIFFRACTION100
1.5134-1.56740.12983060.11185540X-RAY DIFFRACTION100
1.5674-1.63010.1373040.11385552X-RAY DIFFRACTION100
1.6301-1.70420.13912620.1255578X-RAY DIFFRACTION100
1.7042-1.7940.15852870.13255636X-RAY DIFFRACTION100
1.794-1.90620.14283120.14185541X-RAY DIFFRACTION100
1.9062-2.05310.1542720.13945629X-RAY DIFFRACTION100
2.0531-2.25910.14492950.14445618X-RAY DIFFRACTION100
2.2591-2.58480.16063000.16565677X-RAY DIFFRACTION100
2.5848-3.25190.18283110.17465681X-RAY DIFFRACTION100
3.2519-15.81080.15143300.15155885X-RAY DIFFRACTION100

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