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- PDB-8p8s: Recombinant Ym2 crystal structure -

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Basic information

Entry
Database: PDB / ID: 8p8s
TitleRecombinant Ym2 crystal structure
ComponentsChitinase-like protein 4
KeywordsIMMUNE SYSTEM / Ym2 / Chil4 / in vivo crystallization / chitinase-like protein
Function / homology
Function and homology information


chitin binding / carbohydrate metabolic process / 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 4
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.17 Å
AuthorsVerschueren, K.H.G. / Verstraete, K. / Heyndrickx, I. / Smole, U. / Aegerter, A. / 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 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,7867
Polymers47,4131
Non-polymers3726
Water10,485582
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: light scattering, Monomeric in solution as determined via SEC-MALLS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1200 Å2
ΔGint19 kcal/mol
Surface area15280 Å2
Unit cell
Length a, b, c (Å)51.090, 59.900, 59.880
Angle α, β, γ (deg.)90.00, 94.14, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Chitinase-like protein 4 / Chitinase-3-like protein 4 / Secreted protein Ym2


Mass: 47413.102 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: The cDNA sequence encoding murine Ym2 (Uniprot Q91Z98, residues 22 - 402) was cloned in the pTwist-CMV-BetaGlobin mammalian expression vector, in frame with the mouse IgH signal peptide ...Details: The cDNA sequence encoding murine Ym2 (Uniprot Q91Z98, residues 22 - 402) was cloned in the pTwist-CMV-BetaGlobin mammalian expression vector, in frame with the mouse IgH signal peptide (MGWSCIIFFLVATATGVHS), and an N-terminal hexahistine-tag followed by a Tobacco Etch Virus (TEV)-protease cleavage site. Ym2 was purified via IMAC and SEC. Before crystallization the His-tag was removed by incubation with TEV protease.
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Chil4, Chi3l4, Ym2 / Plasmid: pTwist_ss_His_TEV_Ym2 / Cell line (production host): HEK293 FreeStyle / Production host: Homo sapiens (human) / References: UniProt: Q91Z98
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 582 / 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: 1.93 Å3/Da / Density % sol: 36.18 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 0.1 M sodium acetate pH 6.0 and 200 mM CaCl / Temp details: Temperature controlled incubator

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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: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 20, 2019
RadiationMonochromator: 0.9763 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.17→59.73 Å / Num. obs: 119183 / % possible obs: 98.4 % / Redundancy: 6.76 % / Biso Wilson estimate: 12.048 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.08 / Net I/σ(I): 15.12
Reflection shellResolution: 1.17→1.24 Å / Mean I/σ(I) obs: 4.74 / Num. unique obs: 18719 / CC1/2: 0.925 / Rrim(I) all: 0.358 / % possible all: 95.9

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSVERSION Mar 15, 2019 BUILT=20190315data reduction
Aimless0.7.4data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.17→37.45 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.964 / SU R Cruickshank DPI: 0.037 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.037 / SU Rfree Blow DPI: 0.037 / SU Rfree Cruickshank DPI: 0.034
RfactorNum. reflection% reflectionSelection details
Rfree0.167 5924 4.97 %RANDOM
Rwork0.158 ---
obs0.158 119181 98.5 %-
Displacement parametersBiso mean: 11.8 Å2
Baniso -1Baniso -2Baniso -3
1--0.867 Å20 Å20.0606 Å2
2--0.2042 Å20 Å2
3---0.6629 Å2
Refine analyzeLuzzati coordinate error obs: 0.12 Å
Refinement stepCycle: 1 / Resolution: 1.17→37.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2976 0 24 584 3584
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.016170HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.0711117HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1332SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes987HARMONIC5
X-RAY DIFFRACTIONt_it6170HARMONIC20
X-RAY DIFFRACTIONt_nbd1SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion5.22
X-RAY DIFFRACTIONt_other_torsion14.25
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion401SEMIHARMONIC5
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_contact7550SEMIHARMONIC4
LS refinement shellResolution: 1.17→1.18 Å / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.1839 124 5.2 %
Rwork0.1893 2260 -
all0.189 2384 -
obs--89.6 %
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)
10.0327-0.04380.02540.1039-0.01930.0035-0.0046-0.00640.0001-0.00720.00420.0173-0.00990.00290.00040.0044-0.0014-0.0012-0.0077-0.0029-0.000334.164918.478411.4558
20.0051-0.05820.05150.18220.00860.0074-0.0116-0.0066-0.01350.00430.0115-0.0034-0.01440.00450.00010.0049-0.0003-0.0044-0.0035-0.0038-0.002151.486210.492519.4579
30.0505-0.0459-0.0010.0567-0.06570.0305-0.01150.0012-0.0010.00620.00530.00480.01610.00280.00620.0053-0.0001-0.0018-0.0071-0.0015-0.003946.7211-2.882115.9983
40.2931-0.1788-0.03480-0.14670.15010.0741-0.0307-0.01430.01020.0499-0.0259-0.0033-0.0149-0.1240.0053-0.00180.01660.00450.0198-0.01229.183-0.56925.0016
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|1 - A|166 }
2X-RAY DIFFRACTION2{ A|167 - A|213 }
3X-RAY DIFFRACTION3{ A|214 - A|356 }
4X-RAY DIFFRACTION4{ A|357 - A|374 }

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