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- PDB-8zaz: Crystal structure of Chitinase 3-like protein 1 -

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Basic information

Entry
Database: PDB / ID: 8zaz
TitleCrystal structure of Chitinase 3-like protein 1
ComponentsChitinase-3-like protein 1
KeywordsSIGNALING PROTEIN / CHI3L1 / Liver fibrosis biomarkers
Function / homology
Function and homology information


response to interleukin-6 / activation of NF-kappaB-inducing kinase activity / cartilage development / positive regulation of peptidyl-threonine phosphorylation / extracellular matrix structural constituent / chitin catabolic process / chitin binding / response to tumor necrosis factor / response to mechanical stimulus / extracellular matrix ...response to interleukin-6 / activation of NF-kappaB-inducing kinase activity / cartilage development / positive regulation of peptidyl-threonine phosphorylation / extracellular matrix structural constituent / chitin catabolic process / chitin binding / response to tumor necrosis factor / response to mechanical stimulus / extracellular matrix / lung development / response to interleukin-1 / positive regulation of interleukin-8 production / specific granule lumen / positive regulation of angiogenesis / cellular response to tumor necrosis factor / carbohydrate binding / carbohydrate metabolic process / positive regulation of ERK1 and ERK2 cascade / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / inflammatory response / apoptotic process / Neutrophil degranulation / perinuclear region of cytoplasm / endoplasmic reticulum / extracellular space / extracellular exosome / 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
2-acetamido-2-deoxy-beta-D-galactopyranose / Chitinase-3-like protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.31 Å
AuthorsZhao, H.L. / Huang, M.D. / Jiang, L.G.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)82070142 China
CitationJournal: To Be Published
Title: Crystal structure of Chitinase 3-like protein 1
Authors: Zhao, H.L. / Huang, M.D. / Jiang, L.G.
History
DepositionApr 25, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 30, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Chitinase-3-like protein 1
B: Chitinase-3-like protein 1
C: Chitinase-3-like protein 1
D: Chitinase-3-like protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)163,0328
Polymers162,1474
Non-polymers8854
Water4,540252
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)109.480, 122.390, 137.110
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Chitinase-3-like protein 1 / 39 kDa synovial protein / Cartilage glycoprotein 39 / CGP-39 / GP-39 / hCGP-39 / YKL-40


Mass: 40536.758 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CHI3L1 / Production host: Mammalia (mammals) / References: UniProt: P36222
#2: Sugar
ChemComp-NGA / 2-acetamido-2-deoxy-beta-D-galactopyranose / N-acetyl-beta-D-galactosamine / 2-acetamido-2-deoxy-beta-D-galactose / 2-acetamido-2-deoxy-D-galactose / 2-acetamido-2-deoxy-galactose / N-ACETYL-D-GALACTOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGalpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-galactopyranosamineCOMMON NAMEGMML 1.0
b-D-GalpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GalNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 252 / 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: 2.83 Å3/Da / Density % sol: 56.58 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 10% PEG8000, 0.5 M NaCl, 0.1 M sodium citrate pH 3.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 13, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 2.31→50.84 Å / Num. obs: 81373 / % possible obs: 100 % / Redundancy: 13.4 % / Rmerge(I) obs: 0.167 / Net I/σ(I): 12.2
Reflection shellResolution: 2.31→2.37 Å / Rmerge(I) obs: 1.844 / Num. unique obs: 5941

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
HKL-3000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.31→49.97 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.922 / SU B: 8.852 / SU ML: 0.204 / Cross valid method: FREE R-VALUE / ESU R: 0.293 / ESU R Free: 0.235
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2568 3961 4.872 %
Rwork0.2013 77336 -
all0.204 --
obs-81297 99.964 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 51.425 Å2
Baniso -1Baniso -2Baniso -3
1--1.866 Å20 Å20 Å2
2---0.668 Å2-0 Å2
3---2.534 Å2
Refinement stepCycle: LAST / Resolution: 2.31→49.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11412 0 60 252 11724
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.01211780
X-RAY DIFFRACTIONr_bond_other_d0.0010.01610848
X-RAY DIFFRACTIONr_angle_refined_deg1.6881.80815956
X-RAY DIFFRACTIONr_angle_other_deg0.5941.76224952
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.33851440
X-RAY DIFFRACTIONr_dihedral_angle_2_deg10.611576
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.339101900
X-RAY DIFFRACTIONr_dihedral_angle_6_deg14.87810544
X-RAY DIFFRACTIONr_chiral_restr0.080.21700
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0214064
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022928
X-RAY DIFFRACTIONr_nbd_refined0.2330.22367
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1990.29801
X-RAY DIFFRACTIONr_nbtor_refined0.1890.25761
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0820.25928
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2190.2364
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0290.23
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2210.230
X-RAY DIFFRACTIONr_nbd_other0.1790.266
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.3710.29
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0920.21
X-RAY DIFFRACTIONr_mcbond_it5.2014.9435772
X-RAY DIFFRACTIONr_mcbond_other5.2014.9435772
X-RAY DIFFRACTIONr_mcangle_it7.6238.8827208
X-RAY DIFFRACTIONr_mcangle_other7.6238.8827209
X-RAY DIFFRACTIONr_scbond_it5.5915.5596008
X-RAY DIFFRACTIONr_scbond_other5.5915.566009
X-RAY DIFFRACTIONr_scangle_it8.5439.9418748
X-RAY DIFFRACTIONr_scangle_other8.5439.9418749
X-RAY DIFFRACTIONr_lrange_it13.23652.98513157
X-RAY DIFFRACTIONr_lrange_other13.23752.99113154
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.31-2.370.3722980.32256310.32459300.9120.92599.98310.301
2.37-2.4350.3582870.30254870.30557760.9170.93699.96540.275
2.435-2.5050.3552700.28153700.28556410.9160.94599.98230.25
2.505-2.5820.3442620.26551980.26854600.9230.9541000.231
2.582-2.6660.3672740.25550440.26153200.9240.95999.96240.218
2.666-2.760.3012560.23748700.2451260.9390.9641000.202
2.76-2.8640.2992220.22247460.22649700.9430.96799.95980.19
2.864-2.980.2852140.21945770.22147910.9480.9691000.188
2.98-3.1120.252150.20643730.20845880.9580.9721000.182
3.112-3.2630.2912390.21741660.22144050.9410.9691000.195
3.263-3.4390.2591940.20240110.20542050.9570.9751000.187
3.439-3.6470.231990.19437700.19639690.9680.981000.183
3.647-3.8970.2151780.18835670.18937450.9710.981000.183
3.897-4.2070.2341630.16933430.17235060.9680.9831000.169
4.207-4.6050.2131510.15930770.16132280.9720.9841000.165
4.605-5.1430.1921290.14828090.1529380.9780.9871000.158
5.143-5.9290.2381490.17924710.18326210.9710.98499.96180.185
5.929-7.2360.2681190.19721210.20122400.9510.9811000.204
7.236-10.1270.187840.14716870.14817710.9740.9871000.168
10.127-49.970.241580.22910180.2310830.960.96499.35360.267

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