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- PDB-8p8t: Ex vivo Ym2 crystal structure -

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Basic information

Entry
Database: PDB / ID: 8p8t
TitleEx vivo 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: 1.71 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 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)45,1132
Polymers45,0211
Non-polymers921
Water4,432246
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: light scattering, Recombinant Ym2 is monomeric in solution as determined via SEC-MALLS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area280 Å2
ΔGint-0 kcal/mol
Surface area15320 Å2
Unit cell
Length a, b, c (Å)51.261, 60.205, 60.173
Angle α, β, γ (deg.)90.00, 94.24, 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: 45020.758 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: Single ex vivo Ym2 crystals were harvested from the BAL fluid of C57BL/6J-Tg(CAG-Gal10)Bla mice. The sequence corresponds to Uniprot ID Q91Z98.
Source: (natural) Mus musculus (house mouse) / Organ: Lung / Plasmid details: BAL fluid / Strain: C57BL/6J-Tg(CAG-Gal10)Bla / References: UniProt: Q91Z98
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 246 / 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: 2.06 Å3/Da / Density % sol: 40.2 % / Description: Plate-like crystals
Crystal growTemperature: 310 K / Method: in cell
Details: Single ex vivo Ym2 crystals were harvested from the BAL fluid of transgenic C57BL/6J-Tg(CAG-Gal10)Bla mice and cryoprotected by a brief soak in PBS + 35% (v/v) glycerol.
Temp details: In vivo (mouse) crystallisation

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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: SLS / Beamline: X06SA / Wavelength: 1.0000089224 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 8, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0000089224 Å / Relative weight: 1
ReflectionResolution: 1.7→60.01 Å / Num. obs: 39074 / % possible obs: 97.7 % / Redundancy: 3.47 % / Biso Wilson estimate: 24.584 Å2 / CC1/2: 0.992 / Rrim(I) all: 0.177 / Net I/σ(I): 6.59
Reflection shellResolution: 1.7→1.81 Å / Mean I/σ(I) obs: 0.96 / Num. unique obs: 6228 / CC1/2: 0.358 / Rrim(I) all: 1.364

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSVERSION Jan 26, 2018 BUILT=20180808data reduction
Aimless0.7.4data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.71→16.78 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.935 / SU R Cruickshank DPI: 0.107 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.11 / SU Rfree Blow DPI: 0.102 / SU Rfree Cruickshank DPI: 0.102
RfactorNum. reflection% reflectionSelection details
Rfree0.205 2014 5.16 %RANDOM
Rwork0.177 ---
obs0.178 39026 97.8 %-
Displacement parametersBiso mean: 19.24 Å2
Baniso -1Baniso -2Baniso -3
1--2.5256 Å20 Å2-1.3217 Å2
2---1.2762 Å20 Å2
3---3.8018 Å2
Refine analyzeLuzzati coordinate error obs: 0.21 Å
Refinement stepCycle: 1 / Resolution: 1.71→16.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2970 0 6 239 3215
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.013101HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.974221HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1044SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes524HARMONIC5
X-RAY DIFFRACTIONt_it3101HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.57
X-RAY DIFFRACTIONt_other_torsion15.6
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion389SEMIHARMONIC5
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_contact3826SEMIHARMONIC4
LS refinement shellResolution: 1.71→1.72 Å / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.2439 -4.48 %
Rwork0.2323 746 -
all0.2328 781 -
obs--89.8 %
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)
10.3257-0.8266-0.24060.3427-0.21371.60860.07990.012-0.0911-0.0387-0.04020.0351-0.1041-0.1056-0.0397-0.0155-0.0145-0.00660.0168-0.0065-0.003332.31862.55778.0254
20.4740.008-0.02640.59690.04280.2188-0.02650.03330.0284-0.050.03350.0682-0.0458-0.0439-0.007-0.06340.0011-0.0065-0.03190.0015-0.052733.703218.60499.2344
33.2248-0.4704-0.54770.51750.03751.06430.0016-0.00610.09820.0925-0.01360.0866-0.1412-0.06430.01190.00940.0034-0.00270.0018-0.0172-0.005436.91826.389718.6676
40.0115-0.2907-0.10681.20350.51220.7976-0.02060.0087-0.0214-0.02890.002-0.0441-0.04030.05350.0187-0.02570.0045-0.0014-0.0015-0.0057-0.019147.978316.023619.875
53.8762-0.2515-1.68362.3948-0.55872.861-0.032-0.0614-0.1208-0.0009-0.0434-0.1984-0.0280.2510.0754-0.0147-0.0062-0.00620.0394-0.01110.052357.9651-1.396417.7604
60.15770.03320.02710.0878-0.23070.2155-0.01160.0437-0.00430.0144-0.0003-0.0040.06130.01890.0119-0.0702-0.0005-0-0.0136-0.0084-0.02850.2938-0.674614.0785
70.7987-0.3808-0.06820.633-0.06650.6477-0.0309-0.0232-0.07170.03140.05870.04620.048-0.0216-0.0279-0.0178-0.01030.00690.00020.00270.002440.5387-4.882719.4364
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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