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- PDB-2ybu: Crystal structure of human acidic chitinase in complex with bisdi... -

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Basic information

Entry
Database: PDB / ID: 2ybu
TitleCrystal structure of human acidic chitinase in complex with bisdionin F
ComponentsACIDIC MAMMALIAN CHITINASE
KeywordsHYDROLASE
Function / homology
Function and homology information


chitin metabolic process / production of molecular mediator involved in inflammatory response / polysaccharide digestion / Digestion of dietary carbohydrate / chitinase activity / endochitinase activity / chitinase / chitin catabolic process / chitin binding / polysaccharide catabolic process ...chitin metabolic process / production of molecular mediator involved in inflammatory response / polysaccharide digestion / Digestion of dietary carbohydrate / chitinase activity / endochitinase activity / chitinase / chitin catabolic process / chitin binding / polysaccharide catabolic process / immune system process / positive regulation of chemokine production / kinase binding / apoptotic process / extracellular space / extracellular region / cytoplasm
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
Chem-CX9 / Acidic mammalian chitinase
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsSutherland, T.E. / Andersen, O.A. / Betou, M. / Eggleston, I.M. / Maizels, R.M. / van Aalten, D. / Allen, J.E.
CitationJournal: Chem. Biol. / Year: 2011
Title: Analyzing airway inflammation with chemical biology: dissection of acidic mammalian chitinase function with a selective drug-like inhibitor.
Authors: Sutherland, T.E. / Andersen, O.A. / Betou, M. / Eggleston, I.M. / Maizels, R.M. / van Aalten, D. / Allen, J.E.
History
DepositionMar 10, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 8, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 14, 2018Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation_author.name
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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 / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ACIDIC MAMMALIAN CHITINASE
B: ACIDIC MAMMALIAN CHITINASE
C: ACIDIC MAMMALIAN CHITINASE
D: ACIDIC MAMMALIAN CHITINASE
E: ACIDIC MAMMALIAN CHITINASE
F: ACIDIC MAMMALIAN CHITINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)260,94924
Polymers255,7606
Non-polymers5,18918
Water20,1591119
1
A: ACIDIC MAMMALIAN CHITINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,4914
Polymers42,6271
Non-polymers8653
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: ACIDIC MAMMALIAN CHITINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,4914
Polymers42,6271
Non-polymers8653
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: ACIDIC MAMMALIAN CHITINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,4914
Polymers42,6271
Non-polymers8653
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: ACIDIC MAMMALIAN CHITINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,4914
Polymers42,6271
Non-polymers8653
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: ACIDIC MAMMALIAN CHITINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,4914
Polymers42,6271
Non-polymers8653
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: ACIDIC MAMMALIAN CHITINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,4914
Polymers42,6271
Non-polymers8653
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)144.781, 149.194, 151.278
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
ACIDIC MAMMALIAN CHITINASE / AMCASE / CHITINASE


Mass: 42626.621 Da / Num. of mol.: 6 / Fragment: CATALYTIC DOMAIN, RESIDUES 21-398
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Organ: LUNG / Plasmid: PPIC9 / Production host: PICHIA PASTORIS (fungus) / Strain (production host): GS115 / References: UniProt: Q9BZP6, chitinase
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-CX9 / 3,7-DIMETHYL-1-[3-(3-METHYL-2,6-DIOXO-9H-PURIN-1-YL)PROPYL]PURINE-2,6-DIONE / BISDIONIN F / 3,7-DIMETHYL-1-[3-(3-METHYL-2,6-DIOXO-2,3,6,7-TETRAHYDRO-1H-PURIN-1-YL)PROPYL]-2,3,6,7-TETRAHYDRO-1H-PURINE-2,6-DIONE


Mass: 386.365 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C16H18N8O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1119 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsACIDIC MAMMALIAN CHITINASE ISOFORM ASP45 ASN47 MET61

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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: 3.2 Å3/Da / Density % sol: 62 % / Description: NONE
Crystal growpH: 7.4 / Details: 75% SATURATED NACL, 0.1 M HEPES PH 7.4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934
DetectorType: ADSC CCD / Detector: CCD / Date: Feb 18, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2.25→20 Å / Num. obs: 154470 / % possible obs: 99.6 % / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Biso Wilson estimate: 31.9 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 14.8
Reflection shellResolution: 2.25→2.33 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.58 / Mean I/σ(I) obs: 2.7 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.5.0102refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1LG2

1lg2


Resolution: 2.25→19.97 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.932 / SU B: 4.931 / SU ML: 0.122 / Cross valid method: THROUGHOUT / ESU R: 0.198 / ESU R Free: 0.176 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.21916 1544 1 %RANDOM
Rwork0.17296 ---
obs0.17343 152900 99.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.703 Å2
Baniso -1Baniso -2Baniso -3
1-0.51 Å20 Å20 Å2
2---1.1 Å20 Å2
3---0.6 Å2
Refinement stepCycle: LAST / Resolution: 2.25→19.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17856 0 372 1119 19347
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.02218828
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.891.95525722
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.06352250
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.25524.898882
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.45152772
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.6481542
X-RAY DIFFRACTIONr_chiral_restr0.1440.22598
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.02114802
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1211.511196
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.095217988
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.37537632
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.0994.57734
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.25→2.308 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.315 124 -
Rwork0.264 11032 -
obs--99.19 %

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