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

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Basic information

Entry
Database: PDB / ID: 8frb
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: 1.7 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 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 6, 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
C: Acidic mammalian chitinase
D: Acidic mammalian chitinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)182,85419
Polymers178,4884
Non-polymers4,36615
Water30,0131666
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)45,4954
Polymers44,6221
Non-polymers8733
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: 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
4
D: 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
MethodPISA
Unit cell
Length a, b, c (Å)91.926, 106.963, 146.492
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

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Acidic mammalian chitinase / AMCase / YNL


Mass: 44621.992 Da / Num. of mol.: 4
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

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Sugars , 3 types, 10 molecules

#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.: 7 / 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-acetylamino-2-deoxy-alpha-L-idopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1 / Source method: obtained synthetically
DescriptorTypeProgram
DGlcpNAcb1-4LIdopNAca1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2121h-1a_1-5_2*NCC/3=O][a2122h-1b_1-5_2*NCC/3=O]/1-2/a4-b1WURCSPDB2Glycan 1.1.0
#4: 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

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Non-polymers , 2 types, 1671 molecules

#5: Chemical
ChemComp-MG / MAGNESIUM ION


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


Mass: 18.015 Da / Num. of mol.: 1666 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.02 Å3/Da / Density % sol: 39.03 %
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 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: 1.7→57.29 Å / Num. obs: 158679 / % possible obs: 99.87 % / Redundancy: 6.4 % / Biso Wilson estimate: 12.46 Å2 / CC1/2: 0.997 / CC star: 0.999 / Rmerge(I) obs: 0.1111 / Rpim(I) all: 0.04745 / Rrim(I) all: 0.121 / Net I/σ(I): 9.09
Reflection shellResolution: 1.7→1.761 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.5593 / Mean I/σ(I) obs: 3.1 / Num. unique obs: 15679 / CC1/2: 0.888 / CC star: 0.97 / Rpim(I) all: 0.2411 / Rrim(I) all: 0.61 / % possible all: 99.88

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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: 1.7→57.29 Å / SU ML: 0.154 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 16.4476
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1777 7987 5.03 %
Rwork0.1424 150679 -
obs0.1441 158666 99.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 15.72 Å2
Refinement stepCycle: LAST / Resolution: 1.7→57.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11774 0 295 1666 13735
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005612707
X-RAY DIFFRACTIONf_angle_d0.917717360
X-RAY DIFFRACTIONf_chiral_restr0.04961863
X-RAY DIFFRACTIONf_plane_restr0.00742218
X-RAY DIFFRACTIONf_dihedral_angle_d11.71224363
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.720.25022600.19014665X-RAY DIFFRACTION94.89
1.72-1.740.2192620.18474998X-RAY DIFFRACTION99.92
1.74-1.760.23782620.18144956X-RAY DIFFRACTION99.96
1.76-1.780.22152640.17935024X-RAY DIFFRACTION99.98
1.78-1.80.22052670.17214986X-RAY DIFFRACTION99.94
1.8-1.830.21092610.16044990X-RAY DIFFRACTION99.96
1.83-1.860.20522480.15695007X-RAY DIFFRACTION99.98
1.86-1.880.21012590.15385012X-RAY DIFFRACTION99.92
1.88-1.910.1952930.14894958X-RAY DIFFRACTION99.89
1.91-1.940.19352430.14864986X-RAY DIFFRACTION99.94
1.94-1.980.18752580.14695022X-RAY DIFFRACTION99.98
1.98-2.010.17312240.14865056X-RAY DIFFRACTION99.91
2.01-2.050.19782730.14684977X-RAY DIFFRACTION99.96
2.05-2.090.16992740.1325009X-RAY DIFFRACTION99.94
2.09-2.140.17772850.13384992X-RAY DIFFRACTION99.96
2.14-2.190.17272510.13375025X-RAY DIFFRACTION99.91
2.19-2.240.17182780.12894983X-RAY DIFFRACTION99.92
2.24-2.310.15782490.12845030X-RAY DIFFRACTION100
2.31-2.370.19042640.13185025X-RAY DIFFRACTION99.96
2.37-2.450.17412730.135037X-RAY DIFFRACTION99.98
2.45-2.540.18142610.13035040X-RAY DIFFRACTION100
2.54-2.640.16922880.1365013X-RAY DIFFRACTION100
2.64-2.760.16852830.13625042X-RAY DIFFRACTION99.98
2.76-2.90.16322810.12965030X-RAY DIFFRACTION99.96
2.9-3.090.17252630.13415093X-RAY DIFFRACTION99.96
3.09-3.320.16182740.14155075X-RAY DIFFRACTION100
3.32-3.660.16492670.13425086X-RAY DIFFRACTION99.98
3.66-4.190.14072890.11755111X-RAY DIFFRACTION99.98
4.19-5.280.13692540.12215174X-RAY DIFFRACTION99.87
5.28-57.290.23992790.21145277X-RAY DIFFRACTION97.9

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