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

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Basic information

Entry
Database: PDB / ID: 8frd
TitleMouse acidic mammalian chitinase, catalytic domain in complex with N,N'-diacetylchitobiose at pH 5.25
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: 1.68 Å
AuthorsDiaz, R.E. / Fraser, J.S.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P30GM124169 United States
Other governmentT29IP0554 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 20, 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)91,4159
Polymers89,2442
Non-polymers2,1717
Water13,295738
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)70.755, 92.451, 104.990
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.: 5 / 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: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 738 / 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: 1.92 Å3/Da / Density % sol: 36.07 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 5.25
Details: 11 mg/mL AMCase catalytic domain 20% w/v PEG 6000 0.1 M Sodium Acetate pH 5.25 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: 1.68→58.67 Å / Num. obs: 78163 / % possible obs: 98.72 % / Redundancy: 6.4 % / Biso Wilson estimate: 11.55 Å2 / CC1/2: 0.993 / CC star: 0.998 / Rmerge(I) obs: 0.1155 / Rpim(I) all: 0.04965 / Rrim(I) all: 0.126 / Net I/σ(I): 9.68
Reflection shellResolution: 1.68→1.74 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.569 / Mean I/σ(I) obs: 3.09 / Num. unique obs: 7593 / CC1/2: 0.68 / CC star: 0.9 / Rpim(I) all: 0.2425 / Rrim(I) all: 0.6197 / % possible all: 97.03

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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: 1.68→58.67 Å / SU ML: 0.1293 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 14.7232
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1678 3883 4.97 %
Rwork0.1391 74277 -
obs0.1405 78153 98.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 14.2 Å2
Refinement stepCycle: LAST / Resolution: 1.68→58.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5880 0 147 751 6778
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00716394
X-RAY DIFFRACTIONf_angle_d0.90998741
X-RAY DIFFRACTIONf_chiral_restr0.0517932
X-RAY DIFFRACTIONf_plane_restr0.00761124
X-RAY DIFFRACTIONf_dihedral_angle_d12.30562210
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.68-1.70.23261160.17192433X-RAY DIFFRACTION91.2
1.7-1.720.19371100.17762602X-RAY DIFFRACTION97.52
1.72-1.740.21371340.16672615X-RAY DIFFRACTION97.72
1.74-1.770.18181380.16212615X-RAY DIFFRACTION98.08
1.77-1.790.21791430.15992592X-RAY DIFFRACTION97.96
1.79-1.820.21651310.15562633X-RAY DIFFRACTION98.12
1.82-1.850.19081340.15412590X-RAY DIFFRACTION97.88
1.85-1.880.19221300.14952643X-RAY DIFFRACTION98.4
1.88-1.910.17991470.14052617X-RAY DIFFRACTION98.43
1.91-1.940.16151270.13452615X-RAY DIFFRACTION98.6
1.94-1.980.15731300.1342644X-RAY DIFFRACTION98.51
1.98-2.020.15271240.12732630X-RAY DIFFRACTION98.46
2.02-2.070.16381530.12822630X-RAY DIFFRACTION98.69
2.07-2.110.16571300.12732651X-RAY DIFFRACTION98.9
2.11-2.170.14411290.12912634X-RAY DIFFRACTION98.96
2.17-2.230.161500.12142649X-RAY DIFFRACTION98.94
2.23-2.290.16011400.1232667X-RAY DIFFRACTION98.8
2.29-2.370.13491410.12332652X-RAY DIFFRACTION98.73
2.37-2.450.16451450.12472657X-RAY DIFFRACTION99.26
2.45-2.550.1741440.12662649X-RAY DIFFRACTION99.47
2.55-2.660.16121520.1322658X-RAY DIFFRACTION99.29
2.66-2.810.16911620.13182688X-RAY DIFFRACTION99.58
2.81-2.980.14471330.13912704X-RAY DIFFRACTION99.65
2.98-3.210.17291360.14122713X-RAY DIFFRACTION99.75
3.21-3.530.17091360.13252735X-RAY DIFFRACTION99.83
3.53-4.050.11751530.12542723X-RAY DIFFRACTION99.86
4.05-5.10.16741670.12372763X-RAY DIFFRACTION99.93
5.1-58.670.22731480.20542875X-RAY DIFFRACTION98.66

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