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- PDB-8p8q: Recombinant Ym1 crystal structure -

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Basic information

Entry
Database: PDB / ID: 8p8q
TitleRecombinant Ym1 crystal structure
ComponentsChitinase-like protein 3
KeywordsIMMUNE SYSTEM / Ym1 / Chil3 / Chitinase-like protein
Function / homology
Function and homology information


rough endoplasmic reticulum lumen / beta-N-acetylhexosaminidase / beta-N-acetylhexosaminidase activity / : / chitin catabolic process / chitin binding / polysaccharide catabolic process / nuclear envelope / cytoplasmic vesicle / carbohydrate binding ...rough endoplasmic reticulum lumen / beta-N-acetylhexosaminidase / beta-N-acetylhexosaminidase activity / : / chitin catabolic process / chitin binding / polysaccharide catabolic process / nuclear envelope / cytoplasmic vesicle / carbohydrate binding / inflammatory response / extracellular region / cytoplasm
Similarity search - Function
: / 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
ACETATE ION / Chitinase-like protein 3
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.792 Å
AuthorsVerschueren, K.H.G. / Verstraete, K. / Heyndrickx, I. / Aegerter, H. / Smole, U. / 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 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: Chitinase-like protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,5403
Polymers44,3891
Non-polymers1512
Water3,963220
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: light scattering, Predominantly monomeric at low concentration (in PBS buffer). Self-association at higher concentrations (> 0.3 mg/mL)
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area500 Å2
ΔGint-1 kcal/mol
Surface area15150 Å2
Unit cell
Length a, b, c (Å)50.331, 60.009, 60.115
Angle α, β, γ (deg.)90.00, 94.66, 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: 44388.898 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Recombinant Ym1 (Uniprot ID O35744, residues 22 - 398) was secreted from HEK293 FreeStyle cells and purified via ion exchange chromatography and SEC. The mouse IgH signal peptide ...Details: Recombinant Ym1 (Uniprot ID O35744, residues 22 - 398) was secreted from HEK293 FreeStyle cells and purified via ion exchange chromatography and SEC. The mouse IgH signal peptide (MGWSCIIFFLVATATGVHS) was used as a secretion signal.
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Chil3, Chi3l3, Ym1 / Plasmid: pCAGGSs_Ym1
Details (production host): Ym1 residues 22 to 398 in frame with the mouse IgH signal peptide
Cell line (production host): HEK293 FreeStyle / Production host: Homo sapiens (human) / References: UniProt: O35744, beta-N-acetylhexosaminidase
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 220 / 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: 2.04 Å3/Da / Density % sol: 39.66 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Condition A7 of the Hampton Research Crystal Screen HT (0.1 M sodium cacodylate pH 6.5, 1.4 M sodium acetate) Cryo-protection: mother liquor supplemented with 30% (v/v) glycerol

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: Cold N2 gas stream / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97857 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 5, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 1.79→59.92 Å / Num. obs: 33407 / % possible obs: 99.2 % / Redundancy: 4.06 % / Biso Wilson estimate: 20.318 Å2 / CC1/2: 0.979 / Rrim(I) all: 0.247 / Net I/σ(I): 5.28
Reflection shellResolution: 1.79→1.9 Å / Mean I/σ(I) obs: 1.54 / Num. unique obs: 5172 / CC1/2: 0.566 / Rrim(I) all: 1.121 / % possible all: 96

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Processing

Software
NameVersionClassification
BUSTER2.10.3 (6-FEB-2020)refinement
XDSVERSION Jan 26, 2018 BUILT=20180808data reduction
Aimlessversion 0.7.4data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.792→42.4 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.894 / SU R Cruickshank DPI: 0.122 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.124 / SU Rfree Blow DPI: 0.11 / SU Rfree Cruickshank DPI: 0.11
RfactorNum. reflection% reflectionSelection details
Rfree0.1986 1650 4.94 %RANDOM
Rwork0.1729 ---
obs0.1742 33407 99.2 %-
Displacement parametersBiso mean: 12.8 Å2
Baniso -1Baniso -2Baniso -3
1--5.2058 Å20 Å2-1.5844 Å2
2--1.668 Å20 Å2
3---3.5378 Å2
Refine analyzeLuzzati coordinate error obs: 0.23 Å
Refinement stepCycle: LAST / Resolution: 1.792→42.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2957 0 10 215 3182
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0083090HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.914212HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1031SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes522HARMONIC5
X-RAY DIFFRACTIONt_it3079HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.77
X-RAY DIFFRACTIONt_other_torsion14.61
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion387SEMIHARMONIC5
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_contact2952SEMIHARMONIC4
LS refinement shellResolution: 1.792→1.81 Å
RfactorNum. reflection% reflection
Rfree0.2131 -3.89 %
Rwork0.2233 643 -
obs--75.94 %
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)
10.8496-0.5736-0.0141.33362.34874.48390.10870.0239-0.0832-0.0407-0.02880.1099-0.0326-0.1579-0.07990.0545-0.0029-0.040.02210.00570.05430.91142.98488.3568
20.57810.03430.12210.8487-0.07560.4309-0.02710.00950.0353-0.13040.03710.0695-0.0362-0.0412-0.0101-0.0380.0055-0.0229-0.04650.0006-0.034632.333418.40169.33
34.8686-1.1159-0.54650.79350.22421.4412-0.0459-0.04990.27930.04860.04590.0633-0.1434-0.103-00.017-0.002-0.0211-0.005-0.0069-0.02235.856926.48218.6893
40.7086-0.9471-0.57792.12381.10531.1225-0.0287-0.012-0.0191-0.0726-0.0094-0.0272-0.03990.05160.0381-0.03980.0181-0.0172-0.03780.0065-0.042746.740515.828619.9486
53.65890.2869-1.16612.10110.28343.0921-0.03780.1046-0.1232-0.0503-0-0.27720.05880.10020.03780.00650.00890.00130.01560.01660.067956.4762-1.487517.7185
60.2636-0.258-0.17420.60920.15650.44090.01710.00960.00280.0143-0.0001-0.02740.05010.0164-0.0171-0.02340.0017-0.015-0.0193-0.002-0.001548.956-0.219314.2793
70.8381-0.5022-0.12140.68920.05260.6042-0.00460.0143-0.09170.02520.01380.04750.0741-0.0245-0.0092-0.0224-0.0188-0.0068-0.03150.00640.000139.5651-5.105619.1511
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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