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- PDB-6ldu: Crystal structure of CeCht1, a nematode I family chitinase from C... -

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Basic information

Entry
Database: PDB / ID: 6ldu
TitleCrystal structure of CeCht1, a nematode I family chitinase from C. elegans
ComponentsProbable endochitinase
KeywordsHYDROLASE / Nematode chitinase
Function / homology
Function and homology information


Digestion of dietary carbohydrate / ATF6-mediated unfolded protein response / Neutrophil degranulation / response to fungus / chitinase activity / endochitinase activity / chitinase / 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 ...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. / Glycosyl hydrolases family 18 / Glycoside hydrolase family 18, catalytic domain / Glycoside hydrolase superfamily
Similarity search - Domain/homology
Probable endochitinase
Similarity search - Component
Biological speciesCaenorhabditis elegans (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.701 Å
AuthorsChen, Q. / Yang, Q. / Zhou, Y.
CitationJournal: To Be Published
Title: Crystal structure of CeCht1, a nematode I family chitinase from C. elegans
Authors: Chen, Q. / Yang, Q. / Zhou, Y.
History
DepositionNov 23, 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
Revision 1.2Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)42,7794
Polymers42,3731
Non-polymers4053
Water8,881493
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area700 Å2
ΔGint1 kcal/mol
Surface area14750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.571, 66.935, 57.352
Angle α, β, γ (deg.)90.000, 102.709, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Probable endochitinase


Mass: 42373.312 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: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 493 / 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: 2.1 Å3/Da / Density % sol: 41.56 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: PEG 3.350, Tris

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9778 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 21, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9778 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 38049 / % possible obs: 99 % / Redundancy: 3.3 % / Biso Wilson estimate: 12.8025320272 Å2 / Rmerge(I) obs: 0.083 / Net I/σ(I): 9.199
Reflection shellResolution: 1.7→1.73 Å / Rmerge(I) obs: 0.401 / Num. unique obs: 3724

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3W4R

3w4r


Resolution: 1.701→42.927 Å / SU ML: 0.16279252798 / Cross valid method: FREE R-VALUE / σ(F): 1.34013105416 / Phase error: 19.1992084172
RfactorNum. reflection% reflection
Rfree0.208848124346 2000 5.25637993114 %
Rwork0.166080997391 --
obs0.168286066436 38049 98.5189404728 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 15.5496121088 Å2
Refinement stepCycle: LAST / Resolution: 1.701→42.927 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2994 0 26 493 3513
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006794669913483113
X-RAY DIFFRACTIONf_angle_d0.9062166661344240
X-RAY DIFFRACTIONf_chiral_restr0.0586631307443435
X-RAY DIFFRACTIONf_plane_restr0.00620318966322546
X-RAY DIFFRACTIONf_dihedral_angle_d16.32697039651081
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7011-1.74370.2263522605211380.1927401056562480X-RAY DIFFRACTION95.6172388605
1.7437-1.79080.258901044811430.1870119235812587X-RAY DIFFRACTION98.948894527
1.7908-1.84350.2266368386611430.1772925855472582X-RAY DIFFRACTION99.3800145879
1.8435-1.9030.2299216366381440.1734120089222590X-RAY DIFFRACTION99.671892089
1.903-1.9710.2232286064861430.1631446491862589X-RAY DIFFRACTION99.5989792198
1.971-2.04990.2403307961851440.1612455157582592X-RAY DIFFRACTION99.5271007639
2.0499-2.14320.1935503538411450.1571829079232600X-RAY DIFFRACTION99.4925697717
2.1432-2.25620.2160299121141430.1549442454982579X-RAY DIFFRACTION99.5975118917
2.2562-2.39760.2104426841191430.1648711070232594X-RAY DIFFRACTION99.4188158373
2.3976-2.58270.2136486932511450.1672851290782602X-RAY DIFFRACTION99.4209192906
2.5827-2.84250.2014930828451450.1647495791152599X-RAY DIFFRACTION99.2405063291
2.8425-3.25370.1856482068931420.1671415093252575X-RAY DIFFRACTION98.5849056604
3.2537-4.09880.1866991398431400.1552929423272535X-RAY DIFFRACTION95.8781362007
4.0988-42.92660.21286917011420.1731389700892545X-RAY DIFFRACTION95.0141442716

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