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

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Basic information

Entry
Database: PDB / ID: 8gca
TitleMouse acidic mammalian chitinase, catalytic domain in complex with N,N',N''-triacetylchitotriose at pH 4.74
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
triacetyl-beta-chitotriose / 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
DepositionMar 1, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 15, 2023Provider: repository / Type: Initial release
Revision 2.0Jun 7, 2023Group: Atomic model / Derived calculations / Category: atom_site / struct_conn
Item: _atom_site.label_alt_id / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id
Revision 2.1Jun 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 2.2Jul 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 2.3Apr 10, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / citation / Item: _citation.year
Revision 2.4Nov 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

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Assembly

Deposited unit
A: Acidic mammalian chitinase
B: Acidic mammalian chitinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,2038
Polymers89,2442
Non-polymers2,9596
Water18,5371029
1
A: Acidic mammalian chitinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,5054
Polymers44,6221
Non-polymers1,8833
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Acidic mammalian chitinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,6984
Polymers44,6221
Non-polymers1,0763
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)76.066, 91.719, 106.132
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-(1-4)-2- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide, Oligosaccharide / Class: Inhibitor / Mass: 627.594 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: triacetyl-beta-chitotriose
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,3,2/[a2122h-1b_1-5_2*NCC/3=O]/1-1-1/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
#3: 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.: 1 / 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
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1029 / 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: 2.07 Å3/Da / Density % sol: 40.7 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 4.74
Details: 11 mg/mL AMCase catalytic domain, 20% w/v PEG 6000, 0.1 M Sodium Acetate pH 4.74, 0.2 M Magnesium Chloride, 12.67 mM GlcNAc3

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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: 1.7→61.83 Å / Num. obs: 82111 / % possible obs: 99.72 % / Redundancy: 6.3 % / Biso Wilson estimate: 12.16 Å2 / CC1/2: 0.997 / CC star: 0.999 / Rmerge(I) obs: 0.1811 / Rpim(I) all: 0.07709 / Rrim(I) all: 0.1972 / Net I/σ(I): 8.83
Reflection shellResolution: 1.7→1.761 Å / Redundancy: 6 % / Rmerge(I) obs: 1.138 / Mean I/σ(I) obs: 3.12 / Num. unique obs: 8079 / CC1/2: 0.805 / CC star: 0.944 / Rpim(I) all: 0.4917 / Rrim(I) all: 1.242 / % possible all: 99.42

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Processing

Software
NameVersionClassification
phenix.refine1.20.1_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→61.83 Å / SU ML: 0.1756 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 21.3286
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1964 4143 5.05 %
Rwork0.159 77938 -
obs0.1609 82081 99.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 16.09 Å2
Refinement stepCycle: LAST / Resolution: 1.7→61.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6014 0 202 1034 7250
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00796505
X-RAY DIFFRACTIONf_angle_d1.05028892
X-RAY DIFFRACTIONf_chiral_restr0.0551950
X-RAY DIFFRACTIONf_plane_restr0.00971135
X-RAY DIFFRACTIONf_dihedral_angle_d12.13722219
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.720.31751450.25652442X-RAY DIFFRACTION96.03
1.72-1.740.26661470.2462588X-RAY DIFFRACTION99.96
1.74-1.760.30951300.22842534X-RAY DIFFRACTION99.4
1.76-1.780.25251210.21552578X-RAY DIFFRACTION99.12
1.78-1.810.24321400.2162566X-RAY DIFFRACTION99.93
1.81-1.830.22731480.19272579X-RAY DIFFRACTION99.74
1.83-1.860.25711290.18512579X-RAY DIFFRACTION99.74
1.86-1.880.24291430.18152526X-RAY DIFFRACTION99.85
1.88-1.910.19161450.17322589X-RAY DIFFRACTION99.78
1.91-1.950.24511160.16792617X-RAY DIFFRACTION99.71
1.95-1.980.22711380.17342571X-RAY DIFFRACTION99.89
1.98-2.010.1971310.17012585X-RAY DIFFRACTION99.78
2.01-2.050.2251430.16342568X-RAY DIFFRACTION99.89
2.05-2.10.19651400.15352597X-RAY DIFFRACTION99.89
2.1-2.140.20361480.1562577X-RAY DIFFRACTION99.82
2.14-2.190.21561390.16152575X-RAY DIFFRACTION99.78
2.19-2.250.19621390.15472607X-RAY DIFFRACTION99.89
2.25-2.310.18841370.1472592X-RAY DIFFRACTION99.71
2.31-2.370.17861290.14662593X-RAY DIFFRACTION99.78
2.37-2.450.19721440.1442566X-RAY DIFFRACTION99.6
2.45-2.540.18911160.14642653X-RAY DIFFRACTION99.82
2.54-2.640.19541260.1492596X-RAY DIFFRACTION99.82
2.64-2.760.20221340.15162613X-RAY DIFFRACTION99.75
2.76-2.910.18491440.14762618X-RAY DIFFRACTION99.75
2.91-3.090.18261420.14952592X-RAY DIFFRACTION99.49
3.09-3.330.19171470.15162638X-RAY DIFFRACTION99.82
3.33-3.660.14991300.13162648X-RAY DIFFRACTION100
3.66-4.190.15681560.12452657X-RAY DIFFRACTION99.89
4.19-5.280.13981460.12812672X-RAY DIFFRACTION99.65
5.28-61.830.2131500.19452822X-RAY DIFFRACTION99.53

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