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- PDB-4p8u: The crystal structures of YKL-39 in the absence of chitooligosacc... -

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Basic information

Entry
Database: PDB / ID: 4p8u
TitleThe crystal structures of YKL-39 in the absence of chitooligosaccharides was solved to resolutions of 2.4 angstrom
ComponentsChitinase-3-like protein 2
KeywordsSUGAR BINDING PROTEIN / chitinase 3-like protein 2 / human YKL-39 / family-18 chitinase
Function / homology
Function and homology information


chitin catabolic process / chitin binding / carbohydrate binding / carbohydrate metabolic process / hydrolase activity / extracellular space / extracellular region
Similarity search - Function
Chitinase A; domain 3 - #10 / Chitinase insertion domain superfamily / Chitinase II / Glyco_18 / Glycosyl hydrolases family 18 (GH18) domain profile. / Glycoside hydrolase family 18, catalytic domain / Glycosyl hydrolases family 18 / Chitinase A; domain 3 / Glycosidases / Glycoside hydrolase superfamily ...Chitinase A; domain 3 - #10 / Chitinase insertion domain superfamily / Chitinase II / Glyco_18 / Glycosyl hydrolases family 18 (GH18) domain profile. / Glycoside hydrolase family 18, catalytic domain / Glycosyl hydrolases family 18 / Chitinase A; domain 3 / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Roll / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Chitinase-3-like protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsSuginta, W. / Ranok, A. / Robinson, R.C. / Wongsantichon, J.
Funding support Thailand, 1items
OrganizationGrant numberCountry
the Office of the Higher Education CommissionCHE500307 Thailand
CitationJournal: J.Biol.Chem. / Year: 2015
Title: Structural and Thermodynamic Insights into Chitooligosaccharide Binding to Human Cartilage Chitinase 3-like Protein 2 (CHI3L2 or YKL-39).
Authors: Ranok, A. / Wongsantichon, J. / Robinson, R.C. / Suginta, W.
History
DepositionApr 1, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 1, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 17, 2014Group: Database references
Revision 1.2Feb 4, 2015Group: Derived calculations
Revision 1.3Feb 11, 2015Group: Database references
Revision 1.4Dec 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description / Source and taxonomy / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / entity_src_gen / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list / refine_hist / struct_keywords
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_oper_list.symmetry_operation / _refine_hist.number_atoms_solvent / _refine_hist.pdbx_number_atoms_ligand / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein / _struct_keywords.text

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Chitinase-3-like protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,9174
Polymers41,6191
Non-polymers2983
Water3,027168
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)70.764, 70.764, 141.179
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-619-

HOH

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Components

#1: Protein Chitinase-3-like protein 2 / Chondrocyte protein 39 / YKL-39


Mass: 41619.246 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CHI3L2 / Plasmid: pET32a(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q15782
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 168 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.05 Å3/Da / Density % sol: 39.49 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: PEG 3350, Lithium sulfate, Bis Tris / PH range: 5.3-5.9

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Data collection

DiffractionMean temperature: 105 K / Ambient temp details: 105K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 5, 2012
RadiationMonochromator: Rh Coated / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→26.3 Å / Num. obs: 13746 / % possible obs: 99.9 % / Redundancy: 7.6 % / Net I/av σ(I): 4.5 / Net I/σ(I): 35.6
Reflection shellResolution: 2.4→2.44 Å / Redundancy: 7.6 % / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 4.5 / % possible all: 99.9

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Processing

SoftwareName: REFMAC / Version: 5.7.0032 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→26.27 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.939 / SU B: 13.32 / SU ML: 0.279 / Cross valid method: FREE R-VALUE / ESU R: 0.781 / ESU R Free: 0.282 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24274 705 4.9 %RANDOM
Rwork0.216 ---
obs0.2173 13746 98.72 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 66.21 Å2
Baniso -1Baniso -2Baniso -3
1-0.58 Å20 Å20 Å2
2--0.58 Å20 Å2
3----1.16 Å2
Refinement stepCycle: 1 / Resolution: 2.4→26.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2896 0 17 168 3081
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0192990
X-RAY DIFFRACTIONr_bond_other_d0.0050.022797
X-RAY DIFFRACTIONr_angle_refined_deg1.391.9534051
X-RAY DIFFRACTIONr_angle_other_deg0.7933.0016459
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3065364
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.52924.809131
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.03215506
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.379157
X-RAY DIFFRACTIONr_chiral_restr0.070.2435
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0213358
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02695
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.1646.4521459
X-RAY DIFFRACTIONr_mcbond_other4.1646.451458
X-RAY DIFFRACTIONr_mcangle_it6.1769.6751822
X-RAY DIFFRACTIONr_mcangle_other6.1749.6771823
X-RAY DIFFRACTIONr_scbond_it4.6956.8111531
X-RAY DIFFRACTIONr_scbond_other4.6916.8111531
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.06910.0712230
X-RAY DIFFRACTIONr_long_range_B_refined9.61753.8623784
X-RAY DIFFRACTIONr_long_range_B_other9.56453.6573754
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.404→2.467 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.346 56 -
Rwork0.42 961 -
obs--97.32 %

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