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

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Basic information

Entry
Database: PDB / ID: 8frg
TitleMouse acidic mammalian chitinase, catalytic domain in complex with N,N'-diacetylchitobiose at pH 5.43
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: 1.74 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 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 1.4Oct 23, 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)90,9908
Polymers89,2442
Non-polymers1,7466
Water15,133840
1
A: Acidic mammalian chitinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,5195
Polymers44,6221
Non-polymers8974
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
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)92.893, 105.041, 70.812
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z

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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.: 3 / Source method: isolated from a natural source
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: 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.: 1 / Source method: isolated from a natural source
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.: 2 / Source method: isolated from a natural source / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 840 / 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: 36.45 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 5.43
Details: 11 mg/mL AMCase catalytic domain 20% w/v PEG 6000 0.1 M Sodium Acetate pH 5.43 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 PILATUS 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: 1.74→69.59 Å / Num. obs: 71369 / % possible obs: 99.56 % / Redundancy: 5.9 % / Biso Wilson estimate: 15.76 Å2 / CC1/2: 0.994 / CC star: 0.998 / Rmerge(I) obs: 0.1321 / Rpim(I) all: 0.05843 / Rrim(I) all: 0.1448 / Net I/σ(I): 6.18
Reflection shellResolution: 1.74→1.803 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.4674 / Mean I/σ(I) obs: 2.56 / Num. unique obs: 37138 / CC1/2: 0.845 / CC star: 0.957 / Rpim(I) all: 0.2207 / Rrim(I) all: 0.5188 / % possible all: 99.05

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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: 1.74→69.59 Å / SU ML: 0.1819 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 20.5198
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2081 3561 4.99 %
Rwork0.1656 67734 -
obs0.1677 71295 99.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 17.9 Å2
Refinement stepCycle: LAST / Resolution: 1.74→69.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5880 0 118 851 6849
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00836724
X-RAY DIFFRACTIONf_angle_d0.95239233
X-RAY DIFFRACTIONf_chiral_restr0.0541978
X-RAY DIFFRACTIONf_plane_restr0.00771204
X-RAY DIFFRACTIONf_dihedral_angle_d12.94612355
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.74-1.760.28081270.22622655X-RAY DIFFRACTION98.65
1.76-1.790.27411460.21852644X-RAY DIFFRACTION99.5
1.79-1.820.26591340.21042681X-RAY DIFFRACTION98.95
1.82-1.850.27091330.19942703X-RAY DIFFRACTION99.93
1.85-1.880.25061320.19112677X-RAY DIFFRACTION99.72
1.88-1.910.2171480.18192667X-RAY DIFFRACTION99.75
1.91-1.940.23021330.17522713X-RAY DIFFRACTION99.72
1.94-1.980.24651300.17652698X-RAY DIFFRACTION99.4
1.98-2.020.21441420.16782696X-RAY DIFFRACTION99.93
2.02-2.060.23561380.17482675X-RAY DIFFRACTION99.89
2.06-2.110.22581390.16722714X-RAY DIFFRACTION100
2.11-2.160.22171400.172689X-RAY DIFFRACTION99.89
2.17-2.220.2181470.1622695X-RAY DIFFRACTION99.72
2.22-2.290.21461710.16312672X-RAY DIFFRACTION99.48
2.29-2.360.20991320.15882687X-RAY DIFFRACTION99.86
2.36-2.450.24011510.16152736X-RAY DIFFRACTION99.93
2.45-2.550.21611570.16632684X-RAY DIFFRACTION99.93
2.55-2.660.24841410.1692713X-RAY DIFFRACTION99.83
2.66-2.80.18891380.16582733X-RAY DIFFRACTION99.83
2.8-2.980.22551600.17222713X-RAY DIFFRACTION99.72
2.98-3.210.19581460.17242732X-RAY DIFFRACTION99.52
3.21-3.530.18261310.14772749X-RAY DIFFRACTION99.65
3.53-4.040.15621410.13292732X-RAY DIFFRACTION98.46
4.04-5.090.13621370.12932778X-RAY DIFFRACTION98.68
5.09-69.590.24011670.1982898X-RAY DIFFRACTION99.22

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