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- PDB-8p8r: Ex vivo Ym1 crystal structure -

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Basic information

Entry
Database: PDB / ID: 8p8r
TitleEx vivo Ym1 crystal structure
ComponentsChitinase-like protein 3
KeywordsIMMUNE SYSTEM / Ym1 / autocrystallization / Chil3 / chitinase-like protein
Function / homology
Function and homology information


rough endoplasmic reticulum lumen / beta-N-acetylhexosaminidase activity / beta-N-acetylhexosaminidase / response to selenium ion / response to nematode / chitin binding / polysaccharide catabolic process / nuclear envelope / carbohydrate binding / cytoplasmic vesicle ...rough endoplasmic reticulum lumen / beta-N-acetylhexosaminidase activity / beta-N-acetylhexosaminidase / response to selenium ion / response to nematode / chitin binding / polysaccharide catabolic process / nuclear envelope / carbohydrate binding / cytoplasmic vesicle / inflammatory response / extracellular region / cytoplasm
Similarity search - Function
: / 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
Chitinase-like protein 3
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.42 Å
AuthorsVerschueren, K.H.G. / Verstraete, K. / Heyndrickx, I. / Smole, U. / Aegerter, H. / Savvides, S.N. / Lambrecht, B.N.
Funding supportEuropean Union, Belgium, 2items
OrganizationGrant numberCountry
European Research Council (ERC)789384European Union
Research Foundation - Flanders (FWO)G0H1222N Belgium
Citation
History
DepositionJun 2, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 17, 2024Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Database references / Category: citation / citation_author
Revision 1.2Oct 16, 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: Chitinase-like protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,5652
Polymers44,5031
Non-polymers621
Water2,936163
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: light scattering, Recombinant Ym1 is predominantly monomeric at lower concentrations but SEC-MALLS shows concentration-dependent self-association (> 0.3 mg/ml).
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area220 Å2
ΔGint4 kcal/mol
Surface area15580 Å2
Unit cell
Length a, b, c (Å)50.518, 60.248, 60.116
Angle α, β, γ (deg.)90.00, 94.48, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Chitinase-like protein 3 / Beta-N-acetylhexosaminidase Ym1 / Chitinase-3-like protein 3 / ECF-L / Eosinophil chemotactic ...Beta-N-acetylhexosaminidase Ym1 / Chitinase-3-like protein 3 / ECF-L / Eosinophil chemotactic cytokine / Secreted protein Ym1


Mass: 44503.148 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: The sequence corresponds to Uniprot ID O35744. Residues 1 to 21 correspond to the native secretion signal. Ym1 crystals were harvested from the BAL fluid of viable motheaten mice (mev/mev mice).
Source: (natural) Mus musculus (house mouse)
Plasmid details: Ym1 crystals were harvested from the BAL fluid of viable motheaten mice (mev/mev mice).
Strain: mev/mev / Tissue: Lung BAL fluid / References: UniProt: O35744, beta-N-acetylhexosaminidase
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 163 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.05 Å3/Da / Density % sol: 39.98 %
Crystal growTemperature: 310 K / Method: in cell
Details: Spontaneous in vivo crystallisation. Single ex vivo Ym1 crystals were harvested from the BAL fluid of mev/mev mice using mounted cryo-loops.
Temp details: In vivo - lung of mice

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: Cold nitrogen gas stream / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 22, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.42→59.9 Å / Num. obs: 66956 / % possible obs: 98.1 % / Redundancy: 3.33 % / Biso Wilson estimate: 20.936 Å2 / CC1/2: 0.998 / Rrim(I) all: 0.055 / Net I/σ(I): 7.2
Reflection shellResolution: 1.42→1.5 Å / Mean I/σ(I) obs: 1.19 / Num. unique obs: 10672 / CC1/2: 0.395 / Rrim(I) all: 1.382

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSVERSION Jan 26, 2018 BUILT=20180808data reduction
Aimlessv. 0.7.4data scaling
PHASERv. 2.8.2phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.42→26.91 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.945 / SU R Cruickshank DPI: 0.062 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.061 / SU Rfree Blow DPI: 0.063 / SU Rfree Cruickshank DPI: 0.063
RfactorNum. reflection% reflectionSelection details
Rfree0.205 3335 4.98 %RANDOM
Rwork0.181 ---
obs0.182 66944 98.2 %-
Displacement parametersBiso mean: 16.01 Å2
Baniso -1Baniso -2Baniso -3
1--3.9093 Å20 Å20.8787 Å2
2--0.9115 Å20 Å2
3---2.9978 Å2
Refine analyzeLuzzati coordinate error obs: 0.18 Å
Refinement stepCycle: 1 / Resolution: 1.42→26.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2957 0 4 163 3124
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.013061HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.984166HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1020SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes515HARMONIC5
X-RAY DIFFRACTIONt_it3061HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion4.03
X-RAY DIFFRACTIONt_other_torsion14.99
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion385SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3702SEMIHARMONIC4
LS refinement shellResolution: 1.42→1.43 Å / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.3005 -5 %
Rwork0.2224 1272 -
all0.2263 1339 -
obs--96.99 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.6508-0.39630.20140.84651.15983.84610.10330.0325-0.0917-0.0305-0.05660.13690.0375-0.3283-0.04680.0214-0.012-0.01330.0025-0.00290.012831.07132.7178.2696
20.46550.0747-0.02530.4828-0.0720.4118-0.04120.02430.0186-0.09880.04170.0596-0.0142-0.053-0.0006-0.0054-0.00260.0069-0.0236-0-0.018232.512118.25079.1887
32.1722-0.4077-0.42160.48660.35380.8691-0.055-0.05150.12890.04380.01310.0279-0.1054-0.06220.0420.01040.0060.0028-0.0145-0.0047-0.023235.931326.328918.695
40.2003-0.4034-0.33350.94140.42270.5039-0.0351-0.0036-0.01970.02780.0057-0.0023-0.02750.03230.029400.00740.0073-0.00560.0013-0.012246.956915.619919.9441
51.7188-0.190.65731.64120.16290.19030.01540.1054-0.0095-0.08720.009-0.2188-0.00310.0671-0.0244-0.01470.00290.0261-0.01230.00520.028356.8303-1.786717.6671
60.3983-0.223-0.0270.57710.05120.46050.00910.03250.0159-0.0013-0.0114-0.02890.04080.02480.0023-0.00560.00010.017-0.00480.00520.001349.2439-0.865614.0124
70.4715-0.3053-0.02820.4692-0.06990.4284-0.0272-0.0066-0.05850.02220.02320.04050.0668-0.05350.0040.0094-0.01140.0134-0.0086-0.00060.004839.5824-5.354719.2668
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|1 - A|24 }
2X-RAY DIFFRACTION2{ A|25 - A|127 }
3X-RAY DIFFRACTION3{ A|128 - A|166 }
4X-RAY DIFFRACTION4{ A|167 - A|195 }
5X-RAY DIFFRACTION5{ A|196 - A|213 }
6X-RAY DIFFRACTION6{ A|214 - A|290 }
7X-RAY DIFFRACTION7{ A|291 - A|373 }

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