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

ID or keywords:

Entry

Database: PDB / ID: 8zaz

Title

Crystal structure of Chitinase 3-like protein 1

Components

Chitinase-3-like protein 1

Keywords

SIGNALING PROTEIN / CHI3L1 / Liver fibrosis biomarkers

Function / homology

Function and homology information

response to interleukin-6 / activation of NF-kappaB-inducing kinase activity / cartilage development / extracellular matrix structural constituent / chitin catabolic process / positive regulation of peptidyl-threonine phosphorylation / chitin binding / response to tumor necrosis factor / response to mechanical stimulus / extracellular matrix ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.31 Å

Authors

Zhao, H.L. / Huang, M.D. / Jiang, L.G.

Funding support

China, 1items

Citation

Journal: To Be Published
Title: Crystal structure of Chitinase 3-like protein 1
Authors: Zhao, H.L. / Huang, M.D. / Jiang, L.G.

History

Deposition	Apr 25, 2024	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Apr 30, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8zaz.cif.gz	304.5 KB	Display	PDBx/mmCIF format
PDB format	pdb8zaz.ent.gz	238.5 KB	Display	PDB format
PDBx/mmJSON format	8zaz.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/za/8zaz ftp://data.pdbj.org/pub/pdb/validation_reports/za/8zaz	HTTPS FTP

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Related structure data

Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI

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

163 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author
Evidence: gel filtration

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 number	19
Space group name H-M	P2₁2₁2₁

#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

Identifier	Type	Program
DGalpNAcb	CONDENSED IUPAC CARBOHYDRATE SYMBOL	GMML 1.0
N-acetyl-b-D-galactopyranosamine	COMMON NAME	GMML 1.0
b-D-GalpNAc	IUPAC CARBOHYDRATE SYMBOL	PDB-CARE 1.0
GalNAc	SNFG CARBOHYDRATE SYMBOL	GMML 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 interest

Y

Has protein modification

Y

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.83 Å³/Da / Density % sol: 56.58 %
Crystal grow	Temperature: 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

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97853 Å
Detector	Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 13, 2023
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97853 Å / Relative weight: 1
Reflection	Resolution: 2.31→50.84 Å / Num. obs: 81373 / % possible obs: 100 % / Redundancy: 13.4 % / R_merge(I) obs: 0.167 / Net I/σ(I): 12.2
Reflection shell	Resolution: 2.31→2.37 Å / R_merge(I) obs: 1.844 / Num. unique obs: 5941

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0425	refinement
HKL-3000		data reduction
HKL-2000		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.31→49.97 Å / Cor.coef. F_o:F_c: 0.954 / Cor.coef. F_o:F_c 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

	R_factor	Num. reflection	% reflection
R_free	0.2568	3961	4.872 %
R_work	0.2013	77336	-
all	0.204	-	-
obs	-	81297	99.964 %

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 51.425 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-1.866 Å²	0 Å²	0 Å²
2-	-	-0.668 Å²	-0 Å²
3-	-	-	2.534 Å²

Refinement step

Cycle: LAST / Resolution: 2.31→49.97 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	11412	0	60	252	11724

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.008	0.012	11780
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	10848
X-RAY DIFFRACTION	r_angle_refined_deg	1.688	1.808	15956
X-RAY DIFFRACTION	r_angle_other_deg	0.594	1.762	24952
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.338	5	1440
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	10.611	5	76
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.339	10	1900
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	14.878	10	544
X-RAY DIFFRACTION	r_chiral_restr	0.08	0.2	1700
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.02	14064
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	2928
X-RAY DIFFRACTION	r_nbd_refined	0.233	0.2	2367
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.199	0.2	9801
X-RAY DIFFRACTION	r_nbtor_refined	0.189	0.2	5761
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.082	0.2	5928
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.219	0.2	364
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.029	0.2	3
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.221	0.2	30
X-RAY DIFFRACTION	r_nbd_other	0.179	0.2	66
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.371	0.2	9
X-RAY DIFFRACTION	r_xyhbond_nbd_other	0.092	0.2	1
X-RAY DIFFRACTION	r_mcbond_it	5.201	4.943	5772
X-RAY DIFFRACTION	r_mcbond_other	5.201	4.943	5772
X-RAY DIFFRACTION	r_mcangle_it	7.623	8.882	7208
X-RAY DIFFRACTION	r_mcangle_other	7.623	8.882	7209
X-RAY DIFFRACTION	r_scbond_it	5.591	5.559	6008
X-RAY DIFFRACTION	r_scbond_other	5.591	5.56	6009
X-RAY DIFFRACTION	r_scangle_it	8.543	9.941	8748
X-RAY DIFFRACTION	r_scangle_other	8.543	9.941	8749
X-RAY DIFFRACTION	r_lrange_it	13.236	52.985	13157
X-RAY DIFFRACTION	r_lrange_other	13.237	52.991	13154

LS refinement shell

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

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	R_factor all	Num. reflection all	Fsc free	Fsc work	% reflection obs (%)	WR_factor R_work
2.31-2.37	0.372	298	0.322	5631	0.324	5930	0.912	0.925	99.9831	0.301
2.37-2.435	0.358	287	0.302	5487	0.305	5776	0.917	0.936	99.9654	0.275
2.435-2.505	0.355	270	0.281	5370	0.285	5641	0.916	0.945	99.9823	0.25
2.505-2.582	0.344	262	0.265	5198	0.268	5460	0.923	0.954	100	0.231
2.582-2.666	0.367	274	0.255	5044	0.261	5320	0.924	0.959	99.9624	0.218
2.666-2.76	0.301	256	0.237	4870	0.24	5126	0.939	0.964	100	0.202
2.76-2.864	0.299	222	0.222	4746	0.226	4970	0.943	0.967	99.9598	0.19
2.864-2.98	0.285	214	0.219	4577	0.221	4791	0.948	0.969	100	0.188
2.98-3.112	0.25	215	0.206	4373	0.208	4588	0.958	0.972	100	0.182
3.112-3.263	0.291	239	0.217	4166	0.221	4405	0.941	0.969	100	0.195
3.263-3.439	0.259	194	0.202	4011	0.205	4205	0.957	0.975	100	0.187
3.439-3.647	0.23	199	0.194	3770	0.196	3969	0.968	0.98	100	0.183
3.647-3.897	0.215	178	0.188	3567	0.189	3745	0.971	0.98	100	0.183
3.897-4.207	0.234	163	0.169	3343	0.172	3506	0.968	0.983	100	0.169
4.207-4.605	0.213	151	0.159	3077	0.161	3228	0.972	0.984	100	0.165
4.605-5.143	0.192	129	0.148	2809	0.15	2938	0.978	0.987	100	0.158
5.143-5.929	0.238	149	0.179	2471	0.183	2621	0.971	0.984	99.9618	0.185
5.929-7.236	0.268	119	0.197	2121	0.201	2240	0.951	0.981	100	0.204
7.236-10.127	0.187	84	0.147	1687	0.148	1771	0.974	0.987	100	0.168
10.127-49.97	0.241	58	0.229	1018	0.23	1083	0.96	0.964	99.3536	0.267

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