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- PDB-8frc: Mouse acidic mammalian chitinase, catalytic domain in complex wit... -

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Basic information

Entry
Database: PDB / ID: 8frc
TitleMouse acidic mammalian chitinase, catalytic domain in complex with N,N'-diacetylchitobiose at pH 4.91
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 (GH18) domain profile. / Glycosyl hydrolases family 18 / 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: 1.92 Å
AuthorsDiaz, R.E. / Fraser, J.S.
Funding support United States, 2items
OrganizationGrant numberCountry
Other governmentT29IP0554
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
DepositionJan 6, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 8, 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 1.4Nov 13, 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
B: Acidic mammalian chitinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,9426
Polymers89,2442
Non-polymers1,6984
Water13,331740
1
A: Acidic mammalian chitinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,4713
Polymers44,6221
Non-polymers8492
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Acidic mammalian chitinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,4713
Polymers44,6221
Non-polymers8492
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)70.933, 92.690, 105.123
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Space group name HallP22ab(z,x,y)
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y+1/2,-z+1/2
#4: -x,-y+1/2,z+1/2

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Components

#1: Protein Acidic mammalian chitinase / AMCase / YNL


Mass: 44621.992 Da / Num. of mol.: 2
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: 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.: 4 / Source method: obtained synthetically
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.: 740 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 1.94 Å3/Da / Density % sol: 36.47 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 4.91
Details: 11 mg/mL AMCase catalytic domain; 20% w/v PEG 6000; 0.1 M Sodium Acetate pH 4.91; 0.2 M Magnesium Chloride; 29.00 mM GlcNAc2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11578 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 15, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11578 Å / Relative weight: 1
ReflectionResolution: 1.92→105.12 Å / Num. obs: 53659 / % possible obs: 100 % / Redundancy: 6.3 % / Biso Wilson estimate: 13.44 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.153 / Rpim(I) all: 0.066 / Rrim(I) all: 0.167 / Net I/σ(I): 7.7
Reflection shellResolution: 1.92→1.95 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.568 / Mean I/σ(I) obs: 3 / Num. unique obs: 2576 / CC1/2: 0.868 / Rpim(I) all: 0.239 / Rrim(I) all: 0.617 / % possible all: 98.6

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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: 1.92→70.93 Å / SU ML: 0.1678 / Cross valid method: FREE R-VALUE / σ(F): 2 / Phase error: 16.6686
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1898 2739 5.11 %
Rwork0.1472 50825 -
obs0.1494 53564 99.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 14.55 Å2
Refinement stepCycle: LAST / Resolution: 1.92→70.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5880 0 116 753 6749
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00676392
X-RAY DIFFRACTIONf_angle_d0.9148738
X-RAY DIFFRACTIONf_chiral_restr0.0487930
X-RAY DIFFRACTIONf_plane_restr0.00761124
X-RAY DIFFRACTIONf_dihedral_angle_d12.77722208
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.92-1.950.21561260.16342450X-RAY DIFFRACTION98.58
1.95-1.990.19771430.15982492X-RAY DIFFRACTION99.96
1.99-2.030.22721420.15172503X-RAY DIFFRACTION99.96
2.03-2.070.1971120.15312539X-RAY DIFFRACTION99.96
2.07-2.110.22411380.14892518X-RAY DIFFRACTION99.96
2.11-2.160.231440.14542500X-RAY DIFFRACTION99.96
2.16-2.220.20181230.14472551X-RAY DIFFRACTION99.93
2.22-2.280.19351410.13372494X-RAY DIFFRACTION100
2.28-2.340.15741340.13192526X-RAY DIFFRACTION99.96
2.34-2.420.18061500.13792526X-RAY DIFFRACTION100
2.42-2.50.16471370.13612529X-RAY DIFFRACTION100
2.5-2.610.21041630.1392491X-RAY DIFFRACTION100
2.61-2.720.21691350.14652556X-RAY DIFFRACTION100
2.72-2.870.18121400.14482526X-RAY DIFFRACTION100
2.87-3.050.20671400.15242547X-RAY DIFFRACTION100
3.05-3.280.18741270.14742569X-RAY DIFFRACTION99.96
3.28-3.610.17731300.13472585X-RAY DIFFRACTION99.93
3.61-4.140.17991280.12922603X-RAY DIFFRACTION100
4.14-5.210.13581310.13152627X-RAY DIFFRACTION100
5.21-70.930.21341550.21852693X-RAY DIFFRACTION98.51

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