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- PDB-9jtr: Crystal Structure of chitinase from the carnivorous plant Drosera... -

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Basic information

Entry
Database: PDB / ID: 9jtr
TitleCrystal Structure of chitinase from the carnivorous plant Drosera adelae
ComponentsBasic chitinase
KeywordsHYDROLASE / chitinase / Class I chitinase / 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: 1.73 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

Downloads & links

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Assembly

Deposited unit
A: Basic chitinase
B: Basic chitinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,3718
Polymers52,6882
Non-polymers6836
Water9,674537
1
A: Basic chitinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,7455
Polymers26,3441
Non-polymers4014
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Basic chitinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,6253
Polymers26,3441
Non-polymers2812
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)73.222, 73.222, 192.998
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Basic chitinase


Mass: 26344.021 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
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: 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.: 2 / Source method: obtained synthetically / 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-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H4O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 537 / 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: 2.83 Å3/Da / Density % sol: 56.61 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.8 M K2HPO4 0.8 M NaH2PO4 0.1 M HEPES pH7.5

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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: 1.73→48.25 Å / Num. obs: 63657 / % possible obs: 100 % / Redundancy: 9.5 % / CC1/2: 1 / Rmerge(I) obs: 0.052 / Rpim(I) all: 0.018 / Rrim(I) all: 0.055 / Χ2: 1.02 / Net I/σ(I): 26.5
Reflection shellResolution: 1.73→1.76 Å / Rmerge(I) obs: 0.787 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 3470 / CC1/2: 0.773 / Rpim(I) all: 0.292 / Rrim(I) all: 0.84 / Χ2: 0.6 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.73→38.43 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.937 / SU B: 2.443 / SU ML: 0.079 / Cross valid method: THROUGHOUT / ESU R: 0.113 / ESU R Free: 0.11 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2382 3145 4.9 %RANDOM
Rwork0.20776 ---
obs0.20929 60440 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.509 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å2-0 Å2
2--0.01 Å2-0 Å2
3----0.02 Å2
Refinement stepCycle: 1 / Resolution: 1.73→38.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3714 0 46 537 4297
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0133874
X-RAY DIFFRACTIONr_bond_other_d0.0010.0183360
X-RAY DIFFRACTIONr_angle_refined_deg1.751.6595278
X-RAY DIFFRACTIONr_angle_other_deg1.5111.5867732
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0675484
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.05723.333204
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.38615524
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.381516
X-RAY DIFFRACTIONr_chiral_restr0.0910.2496
X-RAY DIFFRACTIONr_gen_planes_refined0.010.024640
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02994
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_it2.2692.6771946
X-RAY DIFFRACTIONr_mcbond_other2.2692.6771945
X-RAY DIFFRACTIONr_mcangle_it2.7584.0072424
X-RAY DIFFRACTIONr_mcangle_other2.7574.0082425
X-RAY DIFFRACTIONr_scbond_it3.3362.8991928
X-RAY DIFFRACTIONr_scbond_other3.3352.91929
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.6044.2642855
X-RAY DIFFRACTIONr_long_range_B_refined19.35636.4095010
X-RAY DIFFRACTIONr_long_range_B_other19.41435.7954920
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.73→1.775 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.287 198 -
Rwork0.252 4429 -
obs--100 %

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