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- PDB-9jtp: Crystal Structure of chitinase (E167Q) from the carnivorous plant... -

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Basic information

Entry
Database: PDB / ID: 9jtp
TitleCrystal Structure of chitinase (E167Q) from the carnivorous plant Drosera adelae
ComponentsBasic chitinase
KeywordsHYDROLASE / chitinase / Class I chitinase / E167Q / Drosera adelae
Function / homology
Function and homology information


chitinase activity / chitinase / chitin catabolic process / chitin binding / polysaccharide catabolic process / defense response to fungus / positive regulation of mitotic nuclear division / cell wall macromolecule catabolic process
Similarity search - Function
Chitinases family 19 signature 1. / Chitinases family 19 signature 2. / Glycoside hydrolase, family 19 / Glycoside hydrolase, family 19, catalytic / Chitinase class I / Chitin-binding, type 1, conserved site / Chitin recognition protein / Chitin recognition or binding domain signature. / Chitin-binding type-1 domain profile. / Chitin binding domain ...Chitinases family 19 signature 1. / Chitinases family 19 signature 2. / Glycoside hydrolase, family 19 / Glycoside hydrolase, family 19, catalytic / Chitinase class I / Chitin-binding, type 1, conserved site / Chitin recognition protein / Chitin recognition or binding domain signature. / Chitin-binding type-1 domain profile. / Chitin binding domain / Chitin-binding, type 1 / Endochitinase-like superfamily / Lysozyme-like domain superfamily
Similarity search - Domain/homology
ACETIC ACID / chitinase
Similarity search - Component
Biological speciesDrosera adelae (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.57 Å
AuthorsYoneda, K. / Suizu, Y. / Naruse, Y. / Sakuraba, H. / Ohshima, T.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Crystal Structure of chitin-hydrolyzing enzyme from the carnivorous plant Drosera adelae
Authors: Yoneda, K. / Suizu, Y. / Naruse, Y. / Sakuraba, H. / Ohshima, T.
History
DepositionOct 6, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 13, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Basic chitinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,4032
Polymers26,3431
Non-polymers601
Water2,990166
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)43.120, 63.247, 72.894
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Basic chitinase


Mass: 26343.037 Da / Num. of mol.: 1 / Mutation: E167Q
Source method: isolated from a genetically manipulated source
Details: chitinase / Source: (gene. exp.) Drosera adelae (plant) / Plasmid: pPIC9K / Details (production host): G418-resistant / Production host: Komagataella pastoris (fungus) / Strain (production host): GS115 / References: UniProt: A0A1L7NZT5
#2: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H4O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 166 / 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: 1.89 Å3/Da / Density % sol: 34.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 15% PEG 8000 40% 2-Propanol 0.1 M Imidazole pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 15, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.57→47.77 Å / Num. obs: 26673 / % possible obs: 93.7 % / Redundancy: 5.9 % / Rmerge(I) obs: 0.029 / Rpim(I) all: 0.013 / Rrim(I) all: 0.032 / Net I/σ(I): 33.7
Reflection shellResolution: 1.57→1.6 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.404 / Mean I/σ(I) obs: 2.7 / Num. unique obs: 833 / CC1/2: 0.873 / Rpim(I) all: 0.237 / Rrim(I) all: 0.472 / Χ2: 0.77 / % possible all: 60.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.57→47.77 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.94 / SU B: 2.221 / SU ML: 0.078 / Cross valid method: THROUGHOUT / ESU R: 0.113 / ESU R Free: 0.108 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23438 1303 4.9 %RANDOM
Rwork0.20196 ---
obs0.20358 25329 93.33 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.243 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20 Å20 Å2
2---0.01 Å20 Å2
3----0.01 Å2
Refinement stepCycle: 1 / Resolution: 1.57→47.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1857 0 4 166 2027
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0121919
X-RAY DIFFRACTIONr_bond_other_d0.0010.0181667
X-RAY DIFFRACTIONr_angle_refined_deg1.5971.6482615
X-RAY DIFFRACTIONr_angle_other_deg1.5151.5753834
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3035242
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.15123.333102
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.76715262
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.193158
X-RAY DIFFRACTIONr_chiral_restr0.0820.2243
X-RAY DIFFRACTIONr_gen_planes_refined0.010.022311
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02497
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_it2.032.248972
X-RAY DIFFRACTIONr_mcbond_other2.032.247970
X-RAY DIFFRACTIONr_mcangle_it2.7993.3711212
X-RAY DIFFRACTIONr_mcangle_other2.7983.3711213
X-RAY DIFFRACTIONr_scbond_it2.5252.367947
X-RAY DIFFRACTIONr_scbond_other2.5232.368948
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.6243.5041404
X-RAY DIFFRACTIONr_long_range_B_refined4.88727.3762317
X-RAY DIFFRACTIONr_long_range_B_other4.8327.1032295
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.57→1.611 Å
RfactorNum. reflection% reflection
Rfree0.255 46 -
Rwork-1210 -
obs--61.27 %

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