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- PDB-1hkm: High resolution crystal structure of human chitinase in complex w... -

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Basic information

Entry
Database: PDB / ID: 1hkm
TitleHigh resolution crystal structure of human chitinase in complex with demethylallosamidin
ComponentsCHITOTRIOSIDASE
KeywordsHYDROLASE / HUMAN CHITINASE / CHITIN DEGRADATION / DEMETHYLALLOSAMIDIN
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
METHYL N-ACETYL ALLOSAMINE / Chitotriosidase-1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.55 Å
AuthorsRao, F.V. / Houston, D.R. / Boot, R.G. / Aerts, J.M.F.G. / Sakuda, S. / Van Aalten, D.M.F.
CitationJournal: J.Biol.Chem. / Year: 2003
Title: Crystal Structures of Allosamidin Derivatives in Complex with Human Macrophage Chitinase
Authors: Rao, F.V. / Houston, D.R. / Boot, R.G. / Aerts, J.M.F.G. / Sakuda, S. / Van Aalten, D.M.F.
History
DepositionMar 10, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 11, 2004Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_unobs_or_zero_occ_atoms / struct_asym / struct_conn / 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_seq_id / _atom_site.label_asym_id / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_database_status.status_code_sf / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Dec 13, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 10-STRANDED BARREL THIS IS REPRESENTED BY A 11-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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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)41,4083
Polymers40,7841
Non-polymers6252
Water93752
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)93.827, 93.827, 86.903
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein CHITOTRIOSIDASE / ENDOCHITINASE


Mass: 40783.711 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: GLUCOSE ALLOSAMIDIN B / Source: (natural) HOMO SAPIENS (human) / Cell: MACROPHAGES / References: UniProt: Q13231, chitinase
#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-allopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-allopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DAllpNAcb1-4DAllpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2222h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-AllpNAc]{[(4+1)][b-D-AllpNAc]{}}LINUCSPDB-CARE
#3: Chemical ChemComp-ALI / METHYL N-ACETYL ALLOSAMINE / (4R,5R,6R)-6-(HYDROXYMETHYL)-2-(METHYLENEAMINO)-4,5,6,6A-TETRAHYDRO-3AH-CYCLOPENTA[D][1,3]OXAZOLE-4,5-DIOL


Mass: 200.192 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H12N2O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 52 / 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: 2.5 Å3/Da / Density % sol: 48 %
Crystal growpH: 6.5 / Details: 25 % PEG 550 MME 0.01 M ZNSO4, 0.1 M MES PH 6.5
Crystal grow
*PLUS
pH: 6.5 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
110 mMallosamidin derivative1drop
28 mg/mlprotein1drop
325 %PEG550 MME1reservoir
40.01 M1reservoirZnSO4
50.1 MMES1reservoirpH6.5

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Data collection

DiffractionMean temperature: 113 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorDetector: CCD / Date: Apr 15, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2.55→25 Å / Num. obs: 13215 / % possible obs: 99.6 % / Redundancy: 4.8 % / Biso Wilson estimate: 41.9 Å2 / Rmerge(I) obs: 0.103 / Net I/σ(I): 11.3
Reflection shellResolution: 2.55→2.64 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.642 / Mean I/σ(I) obs: 2.3 / % possible all: 98.9
Reflection
*PLUS
Highest resolution: 2.55 Å / Lowest resolution: 25 Å / Redundancy: 4.8 % / Num. measured all: 63006 / Rmerge(I) obs: 0.103
Reflection shell
*PLUS
% possible obs: 98.9 % / Redundancy: 4.8 % / Num. unique obs: 1283 / Num. measured obs: 6132 / Rmerge(I) obs: 0.642 / Mean I/σ(I) obs: 2.3

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Processing

Software
NameVersionClassification
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MAD
Starting model: PDB ENTRY 1GUV

1guv


Resolution: 2.55→24.93 Å / Rfactor Rfree error: 0.016 / Data cutoff high absF: 1701806.05 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.255 258 2 %RANDOM
Rwork0.213 ---
obs0.213 13091 99.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 36.3798 Å2 / ksol: 0.345866 e/Å3
Displacement parametersBiso mean: 44.4 Å2
Baniso -1Baniso -2Baniso -3
1-8.3 Å20 Å20 Å2
2--8.3 Å20 Å2
3----16.6 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.45 Å0.32 Å
Luzzati d res low-5 Å
Luzzati sigma a0.43 Å0.4 Å
Refinement stepCycle: LAST / Resolution: 2.55→24.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2877 0 42 52 2971
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
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_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.85
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.521.5
X-RAY DIFFRACTIONc_mcangle_it2.482
X-RAY DIFFRACTIONc_scbond_it2.252
X-RAY DIFFRACTIONc_scangle_it3.312.5
LS refinement shellResolution: 2.55→2.71 Å / Rfactor Rfree error: 0.058 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.368 41 2 %
Rwork0.305 2057 -
obs--98.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2DEMETH.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
X-RAY DIFFRACTION4WATER_REP.PARAMDEMETH.TOP
Refinement
*PLUS
Lowest resolution: 25 Å / Rfactor Rfree: 0.257 / Rfactor Rwork: 0.215
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
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.85
LS refinement shell
*PLUS
Lowest resolution: 2.64 Å

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