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- PDB-6le8: Crystal structure of nematode family I chitinase,CeCht1, in compl... -

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Entry
Database: PDB / ID: 6le8
TitleCrystal structure of nematode family I chitinase,CeCht1, in complex with dihydropyrrolopyrazol-6-one derivate 1
ComponentsProbable endochitinase
KeywordsHYDROLASE / Nematode family I chitinase / inhibitor / GH18
Function / homology
Function and homology information


Digestion of dietary carbohydrate / Neutrophil degranulation / response to fungus / chitinase / chitinase activity / chitin catabolic process / chitin binding / polysaccharide catabolic process / extracellular region
Similarity search - Function
Chitin-binding domain type 2 / Chitin binding domain / Chitin binding Peritrophin-A domain / Chitin-binding type-2 domain profile. / Chitin binding domain superfamily / Glycosyl hydrolases family 18 (GH18) active site / Glycosyl hydrolases family 18 (GH18) active site signature. / Chitinase insertion domain superfamily / Chitinase II / Glyco_18 ...Chitin-binding domain type 2 / Chitin binding domain / Chitin binding Peritrophin-A domain / Chitin-binding type-2 domain profile. / Chitin binding domain superfamily / Glycosyl hydrolases family 18 (GH18) active site / Glycosyl hydrolases family 18 (GH18) active site signature. / 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 / Glycoside hydrolase superfamily
Similarity search - Domain/homology
Chem-EAF / Probable endochitinase
Similarity search - Component
Biological speciesCaenorhabditis elegans (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.39909326225 Å
AuthorsChen, Q. / Yang, Q. / Zhou, Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China31801776 China
CitationJournal: To Be Published
Title: Crystal structure of nematode family I chitinase,CeCht1, in complex with dihydropyrrolopyrazol-6-one derivate 1
Authors: Chen, Q. / Yang, Q. / Zhou, Y.
History
DepositionNov 24, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 26, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Probable endochitinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,8194
Polymers42,0911
Non-polymers7283
Water10,881604
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area280 Å2
ΔGint-1 kcal/mol
Surface area13980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.250, 54.727, 139.845
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Space group name HallP22ab(z,x,y)
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y+1/2,-z+1/2
#4: -x,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-618-

HOH

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Components

#1: Protein Probable endochitinase


Mass: 42091.035 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: cht-1, C04F6.3 / Production host: Komagataella phaffii GS115 (fungus) / References: UniProt: Q11174, chitinase
#2: Chemical ChemComp-EAF / (4R)-4-(4-ethoxyphenyl)-3-(2-hydroxyphenyl)-5-(pyridin-3-ylmethyl)-1,4-dihydropyrrolo[3,4-c]pyrazol-6-one


Mass: 426.467 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C25H22N4O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-BTB / 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / BIS-TRIS BUFFER


Mass: 209.240 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C8H19NO5 / Comment: pH buffer*YM
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 604 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.47 Å3/Da / Density % sol: 50.27 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: PEG 3350, Bis-tris, Tris

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97854 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 23, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97854 Å / Relative weight: 1
ReflectionResolution: 1.39→50 Å / Num. obs: 81920 / % possible obs: 98.8 % / Redundancy: 12.9 % / Biso Wilson estimate: 13.2367352268 Å2 / Rmerge(I) obs: 0.088 / Net I/σ(I): 11.819
Reflection shellResolution: 1.4→1.42 Å / Rmerge(I) obs: 0.826 / Num. unique obs: 1059913

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6LDU

6ldu


Resolution: 1.39909326225→27.3635 Å / SU ML: 0.12431504767 / Cross valid method: FREE R-VALUE / σ(F): 1.35098555952 / Phase error: 15.6143668215
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.173038056492 2008 2.45138134362 %
Rwork0.155477821811 79905 -
obs0.155909453924 81913 98.7165272723 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 16.3084852182 Å2
Refinement stepCycle: LAST / Resolution: 1.39909326225→27.3635 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2974 0 52 604 3630
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006602303577363135
X-RAY DIFFRACTIONf_angle_d0.9203240193054274
X-RAY DIFFRACTIONf_chiral_restr0.0830979758267431
X-RAY DIFFRACTIONf_plane_restr0.00618968544102548
X-RAY DIFFRACTIONf_dihedral_angle_d14.66769567161085
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3991-1.43410.2120235577451380.2085742518595456X-RAY DIFFRACTION95.8861844361
1.4341-1.47290.2357482430741400.1890022906545589X-RAY DIFFRACTION98.0321697467
1.4729-1.51620.1675027489081370.1748881481535626X-RAY DIFFRACTION98.2273734447
1.5162-1.56510.1913193233971420.1613442737475627X-RAY DIFFRACTION98.4135107472
1.5651-1.62110.1797791989611440.1581715585735606X-RAY DIFFRACTION98.5263879369
1.6211-1.68590.1968402802611390.1574007299335684X-RAY DIFFRACTION98.7116460417
1.6859-1.76270.1837261436511420.1586701837055692X-RAY DIFFRACTION99.0156143924
1.7627-1.85560.1815988624491450.1556643485775672X-RAY DIFFRACTION99.0802248339
1.8556-1.97180.1766674877311430.1527794420815697X-RAY DIFFRACTION98.7153482082
1.9718-2.1240.1579972729121460.1484986483245723X-RAY DIFFRACTION99.491439227
2.124-2.33760.1715240649751470.1505287476995806X-RAY DIFFRACTION99.6818486269
2.3376-2.67570.1855197164751450.1578925089535759X-RAY DIFFRACTION99.2602555481
2.6757-3.37010.1728236357581470.1572617892665906X-RAY DIFFRACTION99.9669694467
3.3701-27.36350.1519234188221530.14559283356062X-RAY DIFFRACTION98.9177144676

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