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- PDB-8fg7: Apo mouse acidic mammalian chitinase, catalytic domain at 277 K -

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Basic information

Entry
Database: PDB / ID: 8fg7
TitleApo mouse acidic mammalian chitinase, catalytic domain at 277 K
ComponentsAcidic mammalian chitinase
KeywordsHYDROLASE / GH18 chitinase / acidic mammalian chitinase
Function / homology
Function and homology information


Digestion of dietary carbohydrate / production of molecular mediator involved in inflammatory response / chitinase activity / endochitinase activity / chitinase / chitin catabolic process / chitin binding / immune system process / polysaccharide catabolic process / positive regulation of chemokine production ...Digestion of dietary carbohydrate / production of molecular mediator involved in inflammatory response / chitinase activity / endochitinase activity / chitinase / chitin catabolic process / chitin binding / immune system process / polysaccharide catabolic process / positive regulation of chemokine production / apoptotic process / extracellular space / 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 / 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 / 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 / Glycoside hydrolase superfamily
Similarity search - Domain/homology
Acidic mammalian chitinase
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.64 Å
AuthorsDiaz, R.E. / Asthana, P. / Fraser, J.S.
Funding support United States, 2items
OrganizationGrant numberCountry
Other governmentT29IP0554 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P30GM124169 United States
CitationJournal: Biorxiv / Year: 2024
Title: Structural characterization of ligand binding and pH-specific enzymatic activity of mouse Acidic Mammalian Chitinase.
Authors: Diaz, R.E. / Ecker, A.K. / Correy, G.J. / Asthana, P. / Young, I.D. / Faust, B. / Thompson, M.C. / Seiple, I.B. / Van Dyken, S.J. / Locksley, R.M. / Fraser, J.S.
History
DepositionDec 12, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 1, 2023Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.year
Revision 1.2Jul 19, 2023Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title ..._citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.3Apr 10, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / citation / Item: _citation.year
Revision 1.4Oct 9, 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

Downloads & links

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Assembly

Deposited unit
A: Acidic mammalian chitinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,6462
Polymers44,6221
Non-polymers241
Water5,819323
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)63.647, 71.844, 84.672
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Acidic mammalian chitinase / AMCase / YNL


Mass: 44621.992 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Chia, Chia1 / Plasmid: mAMCase_CatD_6xHis_pTwistCMV / Cell line (production host): ExpiCHO-S / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: Q91XA9, chitinase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 323 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.16 Å3/Da / Density % sol: 43.1 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop
Details: 11 mg/mL AMCase catalytic domain 19.8% PEG 3350 0.198 M Magnesium Formate 0.01 M Phenol

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Data collection

DiffractionMean temperature: 277 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.1158 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 20, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1158 Å / Relative weight: 1
ReflectionResolution: 1.64→54.78 Å / Num. obs: 47999 / % possible obs: 99.37 % / Redundancy: 12.9 % / Biso Wilson estimate: 16.6 Å2 / CC1/2: 0.996 / CC star: 0.999 / Rmerge(I) obs: 0.2489 / Rpim(I) all: 0.07097 / Rrim(I) all: 0.2591 / Net I/σ(I): 7
Reflection shellResolution: 1.64→1.699 Å / Redundancy: 13.2 % / Mean I/σ(I) obs: 1.19 / Num. unique obs: 4688 / CC1/2: 0.502 / % possible all: 98.65

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
xia20.3.8.0data reduction
DIALS2.2.10-g6dafd9427-releasedata scaling
PHASER2.8.3phasing
Coot0.9.6model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.64→54.78 Å / SU ML: 0.1929 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 16.3817
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1713 2327 4.85 %
Rwork0.1469 45642 -
obs0.1481 47969 99.37 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 19.41 Å2
Refinement stepCycle: LAST / Resolution: 1.64→54.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3007 0 1 323 3331
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00773204
X-RAY DIFFRACTIONf_angle_d0.96174377
X-RAY DIFFRACTIONf_chiral_restr0.0578447
X-RAY DIFFRACTIONf_plane_restr0.0088573
X-RAY DIFFRACTIONf_dihedral_angle_d12.02611134
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.64-1.670.3231490.28262604X-RAY DIFFRACTION98.25
1.67-1.710.32011160.25712641X-RAY DIFFRACTION98.68
1.71-1.750.25591430.24672629X-RAY DIFFRACTION98.89
1.75-1.790.26031250.23552645X-RAY DIFFRACTION99
1.79-1.840.2411540.20852632X-RAY DIFFRACTION98.97
1.84-1.90.22211450.18922630X-RAY DIFFRACTION99.11
1.9-1.960.21311260.17452655X-RAY DIFFRACTION99.36
1.96-2.030.20031380.16852675X-RAY DIFFRACTION99.58
2.03-2.110.20781230.15752667X-RAY DIFFRACTION99.29
2.11-2.20.16441480.14332671X-RAY DIFFRACTION99.68
2.2-2.320.14881320.13242684X-RAY DIFFRACTION99.44
2.32-2.470.15941310.12762703X-RAY DIFFRACTION99.65
2.47-2.660.15131210.13162734X-RAY DIFFRACTION100
2.66-2.920.15221390.12852708X-RAY DIFFRACTION100
2.92-3.350.15821420.13372729X-RAY DIFFRACTION100
3.35-4.220.13031500.11142750X-RAY DIFFRACTION99.97
4.22-54.780.13651450.12352885X-RAY DIFFRACTION99.38

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