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- PDB-8fr9: Mouse acidic mammalian chitinase, catalytic domain in complex wit... -

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Basic information

Entry
Database: PDB / ID: 8fr9
TitleMouse acidic mammalian chitinase, catalytic domain in complex with N,N'-diacetylchitobiose at pH 5.08
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: 1.5 Å
AuthorsDiaz, R.E. / 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
DepositionJan 6, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 15, 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)91,86311
Polymers89,2442
Non-polymers2,6199
Water18,7721042
1
A: Acidic mammalian chitinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,9205
Polymers44,6221
Non-polymers1,2984
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Acidic mammalian chitinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,9446
Polymers44,6221
Non-polymers1,3225
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)71.113, 92.641, 105.423
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
#3: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-alpha-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 2 / Source method: obtained synthetically
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAca1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1a_1-5_2*NCC/3=O][a2122h-1b_1-5_2*NCC/3=O]/1-2/a4-b1WURCSPDB2Glycan 1.1.0
#4: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 18.015 Da / Num. of mol.: 1042 / 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: 1.95 Å3/Da / Density % sol: 36.78 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 5.08
Details: 11 mg/mL AMCase catalytic domain; 20% w/v PEG 6000; 0.1 M Sodium Acetate pH 5.08; 0.2 M Magnesium Chloride; 19.33 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: 1.5→69.59 Å / Num. obs: 109127 / % possible obs: 97.48 % / Redundancy: 6.4 % / Biso Wilson estimate: 9.16 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.06539 / Rpim(I) all: 0.02784 / Rrim(I) all: 0.07122 / Net I/σ(I): 16.77
Reflection shellResolution: 1.5→1.53 Å / Redundancy: 6 % / Rmerge(I) obs: 0.2976 / Mean I/σ(I) obs: 5.46 / Num. unique obs: 10560 / CC1/2: 0.934 / CC star: 0.985 / Rpim(I) all: 0.1311 / Rrim(I) all: 0.3259 / % possible all: 95.47

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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: 1.5→69.59 Å / SU ML: 0.1036 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 14.3573
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1644 5451 5 %
Rwork0.1376 103676 -
obs0.1389 109127 97.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 12.73 Å2
Refinement stepCycle: LAST / Resolution: 1.5→69.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5994 0 177 1049 7220
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01026671
X-RAY DIFFRACTIONf_angle_d1.09899140
X-RAY DIFFRACTIONf_chiral_restr0.0804985
X-RAY DIFFRACTIONf_plane_restr0.00851169
X-RAY DIFFRACTIONf_dihedral_angle_d12.53912269
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.520.19421600.16373316X-RAY DIFFRACTION93.9
1.52-1.530.20732020.16383311X-RAY DIFFRACTION95.85
1.53-1.550.17791960.15793347X-RAY DIFFRACTION95.52
1.55-1.570.19171800.15573358X-RAY DIFFRACTION95.73
1.57-1.590.19891610.14763369X-RAY DIFFRACTION96.05
1.59-1.620.16311690.1453395X-RAY DIFFRACTION96.19
1.62-1.640.18911750.14593367X-RAY DIFFRACTION95.99
1.64-1.660.16781970.14333363X-RAY DIFFRACTION96.5
1.66-1.690.17861750.13973404X-RAY DIFFRACTION96.42
1.69-1.720.17961780.1423380X-RAY DIFFRACTION96.37
1.72-1.750.19411820.1473404X-RAY DIFFRACTION96.87
1.75-1.780.1571790.14353400X-RAY DIFFRACTION97.02
1.78-1.810.15911630.13913446X-RAY DIFFRACTION97.17
1.81-1.850.18932080.13873394X-RAY DIFFRACTION97.27
1.85-1.890.16562030.13463411X-RAY DIFFRACTION97.33
1.89-1.930.15561720.1293436X-RAY DIFFRACTION97.46
1.93-1.980.16051610.1333469X-RAY DIFFRACTION97.63
1.98-2.040.18561820.1313474X-RAY DIFFRACTION97.78
2.04-2.10.16411730.13143480X-RAY DIFFRACTION97.94
2.1-2.160.16191780.1293467X-RAY DIFFRACTION98.14
2.16-2.240.15451640.12483488X-RAY DIFFRACTION98.33
2.24-2.330.15841870.12343488X-RAY DIFFRACTION98.29
2.33-2.440.15561910.12133485X-RAY DIFFRACTION98.47
2.44-2.560.13441780.1293542X-RAY DIFFRACTION98.94
2.56-2.720.15321730.1363537X-RAY DIFFRACTION98.83
2.72-2.940.17322040.13123538X-RAY DIFFRACTION99.31
2.94-3.230.16721870.14253569X-RAY DIFFRACTION99.29
3.23-3.70.14291880.12923606X-RAY DIFFRACTION99.55
3.7-4.660.1391900.12353640X-RAY DIFFRACTION99.64
4.66-69.590.18451950.1793792X-RAY DIFFRACTION99.28

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