PDB-4wjx: Crystal structure of human chitotriosidase-1 catalytic domain at ...

ID or keywords:

Entry

Database: PDB / ID: 4wjx

Title

Crystal structure of human chitotriosidase-1 catalytic domain at 1.0 A resolution

Components

Chitotriosidase-1

Keywords

HYDROLASE / CHIT1 / GH18 chitinase / protonation states / hydrolysis / catalytic mechanism

Function / homology

Function and homology information

polysaccharide digestion / Digestion of dietary carbohydrate / chitinase activity / endochitinase activity / chitinase / chitin catabolic process / chitin binding / polysaccharide catabolic process / hydrolase activity, hydrolyzing O-glycosyl compounds / response to bacterium ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1 Å

Authors

Fadel, F. / Zhao, Y. / Cachau, R. / Cousido-Siah, A. / Ruiz, F.X. / Harlos, K. / Howard, E. / Mitschler, A. / Podjarny, A.

Citation

Journal: Acta Crystallogr.,Sect.D / Year: 2015
Title: New insights into the enzymatic mechanism of human chitotriosidase (CHIT1) catalytic domain by atomic resolution X-ray diffraction and hybrid QM/MM
Authors: Fadel, F. / Zhao, Y. / Cachau, R. / Cousido-Siah, A. / Ruiz, F.X. / Harlos, K. / Howard, E. / Mitschler, A. / Podjarny, A.

History

Deposition	Oct 1, 2014	Deposition site: RCSB / Processing site: PDBE
Revision 1.0	Jul 8, 2015	Provider: repository / Type: Initial release
Revision 1.1	Jul 15, 2015	Group: Database references
Revision 1.2	Jul 22, 2015	Group: Database references
Revision 1.3	Jan 10, 2024	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4	Oct 9, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4wjx.cif.gz	206.6 KB	Display	PDBx/mmCIF format
PDB format	pdb4wjx.ent.gz	164.7 KB	Display	PDB format
PDBx/mmJSON format	4wjx.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	4wjx_validation.pdf.gz	437.7 KB	Display	wwPDB validaton report
Full document	4wjx_full_validation.pdf.gz	440.5 KB	Display
Data in XML	4wjx_validation.xml.gz	21.3 KB	Display
Data in CIF	4wjx_validation.cif.gz	34.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/wj/4wjx ftp://data.pdbj.org/pub/pdb/validation_reports/wj/4wjx	HTTPS FTP

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Related structure data

Related structure data	4wk9C 4wkaC 4wkfC 4wkhC 1guvS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	5qei-d 4bvx-d 4itm-d 3l5d-1 4trw-2 1zvw-2 1i1h-1 4wka-d 7apm-d 6yhd-d Search similar-shape structures by Omokage search (details) 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
Related items in Molecule of the Month	#74 - Feb 2006 alpha-Amylase similarity (1) #138 - Jun 2011 Glucansucrase similarity (1) #228 - Dec 2018 Directed Evolution of Enzymes similarity (1)

Deposited unit

A: Chitotriosidase-1

hetero molecules

42.5 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	85.690, 105.749, 41.528
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	18
Space group name H-M	P2₁2₁2

#1: Protein	Chitotriosidase-1 / Chitinase-1 Mass: 42224.289 Da / Num. of mol.: 1 / Fragment: catalytic domain, UNP residues 22-387 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CHIT1 / Cell line (production host): HEK293T / Production host: Homo sapiens (human) / References: UniProt: Q13231, chitinase
#2: Chemical	ChemComp-TLA / L(+)-TARTARIC ACID Mass: 150.087 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₄H₆O₆
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 521 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	Y

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Experiment

Experiment	Method: X-RAY DIFFRACTION

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Sample preparation

Crystal	Density Matthews: 2.23 Å³/Da / Density % sol: 44.79 %
Crystal grow	Temperature: 290 K / Method: vapor diffusion, hanging drop Details: 25 % (w/v) polyethylene glycol (PEG) 3350, 0.2 M potassium sodium tartrate (PST) at pH 7.2

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.8 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 28, 2013
Radiation	Monochromator: Bartels Monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.8 Å / Relative weight: 1
Reflection	Resolution: 1→50 Å / Num. obs: 188444 / % possible obs: 92.51 % / Redundancy: 6 % / Net I/σ(I): 27.5
Reflection shell	Resolution: 1→1.04 Å / Redundancy: 2.4 % / Mean I/σ(I) obs: 1.77 / % possible all: 48.18

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Processing

Software

Name	Version	Classification
PHENIX	(phenix.refine: dev_1255)	refinement
HKL-2000		data reduction
HKL-2000		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1GUV

1guv

Resolution: 1→15.259 Å / SU ML: 0.06 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 12.38 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1475	9500	5.04 %
R_work	0.1352	-	-
obs	0.1358	188442	92.51 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 1→15.259 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2909	0	20	521	3450

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.005	3686
X-RAY DIFFRACTION	f_angle_d	1.15	5057
X-RAY DIFFRACTION	f_dihedral_angle_d	14.243	1382
X-RAY DIFFRACTION	f_chiral_restr	0.084	513
X-RAY DIFFRACTION	f_plane_restr	0.006	694

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
0.9999-1.0113	0.2483	128	0.2644	2354	X-RAY DIFFRACTION	37
1.0113-1.0231	0.2382	148	0.2302	2983	X-RAY DIFFRACTION	47
1.0231-1.0356	0.2508	208	0.215	3910	X-RAY DIFFRACTION	61
1.0356-1.0487	0.2318	235	0.2019	4660	X-RAY DIFFRACTION	73
1.0487-1.0625	0.1934	272	0.1863	5220	X-RAY DIFFRACTION	82
1.0625-1.0771	0.1658	318	0.1759	5568	X-RAY DIFFRACTION	88
1.0771-1.0925	0.1792	330	0.156	5970	X-RAY DIFFRACTION	93
1.0925-1.1088	0.155	352	0.1391	6107	X-RAY DIFFRACTION	97
1.1088-1.1261	0.1459	325	0.13	6390	X-RAY DIFFRACTION	99
1.1261-1.1445	0.1286	361	0.1172	6330	X-RAY DIFFRACTION	100
1.1445-1.1643	0.1427	355	0.1106	6356	X-RAY DIFFRACTION	100
1.1643-1.1854	0.1181	355	0.1049	6427	X-RAY DIFFRACTION	100
1.1854-1.2082	0.1324	344	0.1016	6389	X-RAY DIFFRACTION	100
1.2082-1.2329	0.129	353	0.1012	6379	X-RAY DIFFRACTION	100
1.2329-1.2597	0.1179	339	0.0972	6452	X-RAY DIFFRACTION	100
1.2597-1.289	0.1106	331	0.0987	6379	X-RAY DIFFRACTION	100
1.289-1.3212	0.1157	346	0.099	6412	X-RAY DIFFRACTION	100
1.3212-1.3569	0.1136	346	0.0959	6424	X-RAY DIFFRACTION	100
1.3569-1.3968	0.1138	329	0.0975	6445	X-RAY DIFFRACTION	100
1.3968-1.4418	0.1183	320	0.1022	6447	X-RAY DIFFRACTION	100
1.4418-1.4933	0.1135	314	0.1029	6473	X-RAY DIFFRACTION	100
1.4933-1.553	0.126	322	0.1058	6452	X-RAY DIFFRACTION	100
1.553-1.6237	0.129	339	0.1105	6465	X-RAY DIFFRACTION	100
1.6237-1.7091	0.1363	343	0.1208	6464	X-RAY DIFFRACTION	100
1.7091-1.8161	0.1483	344	0.129	6508	X-RAY DIFFRACTION	100
1.8161-1.956	0.1453	362	0.1345	6473	X-RAY DIFFRACTION	100
1.956-2.1524	0.1549	367	0.1345	6498	X-RAY DIFFRACTION	100
2.1524-2.4627	0.1638	345	0.1487	6574	X-RAY DIFFRACTION	100
2.4627-3.0985	0.173	328	0.1677	6613	X-RAY DIFFRACTION	100
3.0985-15.2606	0.1527	341	0.1524	6820	X-RAY DIFFRACTION	99

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