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- PDB-7zya: Structure of Chit33 from Trichoderma harzianum. -

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Basic information

Entry
Database: PDB / ID: 7zya
TitleStructure of Chit33 from Trichoderma harzianum.
ComponentsEndochitinase 33
KeywordsHYDROLASE / Chitinase / endo-chitinase / glycoside hydrolase / fungal chitinase / Thichoderma harzianum / GH18 family / chitooligosaccharide / oligosaccharide / COS / chitin / chitosan / chitintetraose. / HYDROLASE.
Function / homology
Function and homology information


endochitinase activity / chitinase / chitin catabolic process / chitin binding / polysaccharide catabolic process / extracellular region
Similarity search - Function
Chitinase Cts1-like / : / Glycosyl hydrolases family 18 (GH18) active site / Glycosyl hydrolases family 18 (GH18) active site signature. / Glycosyl hydrolases family 18 / Glycosyl hydrolases family 18 (GH18) domain profile. / Glycoside hydrolase family 18, catalytic domain / Glycoside hydrolase superfamily
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Endochitinase 33
Similarity search - Component
Biological speciesTrichoderma harzianum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.12 Å
AuthorsJimenez-Ortega, E. / Sanz-Aparicio, J.
Funding support Spain, 1items
OrganizationGrant numberCountry
Spanish Ministry of Economy and CompetitivenessBIO2016-76601-C3-3-R Spain
CitationJournal: Int J Mol Sci / Year: 2022
Title: Structure-Function Insights into the Fungal Endo -Chitinase Chit33 Depict its Mechanism on Chitinous Material.
Authors: Jimenez-Ortega, E. / Kidibule, P.E. / Fernandez-Lobato, M. / Sanz-Aparicio, J.
History
DepositionMay 24, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 31, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Nov 13, 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

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Assembly

Deposited unit
A: Endochitinase 33
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,0265
Polymers32,6141
Non-polymers4124
Water6,684371
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)65.611, 66.909, 75.317
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Endochitinase 33 / 33 kDa endochitinase / Chitinase 33


Mass: 32613.949 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trichoderma harzianum (fungus) / Gene: chit33 / Production host: Komagataella pastoris (fungus) / References: UniProt: Q12713, chitinase
#2: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 371 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.5 Å3/Da / Density % sol: 50.93 % / Description: Diamond shape
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 20% PEG 1500, 20% Glycerol. Soaking conditions: 23% PEG 1500, 20% Glycerol, 2mM Triacetyl-chitotriose. Cryoprotectant conditions: 30% PEG 1500, 20% glycerol.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97919 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 17, 2018 / Details: KB Mirrors
RadiationMonochromator: Si(111) channel-cut, cryocooled / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97919 Å / Relative weight: 1
ReflectionResolution: 1.12→46.89 Å / Num. obs: 127452 / % possible obs: 99.8 % / Redundancy: 6.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.037 / Rpim(I) all: 0.016 / Net I/σ(I): 20.9
Reflection shellResolution: 1.12→1.14 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.698 / Mean I/σ(I) obs: 2.6 / Num. unique obs: 6255 / CC1/2: 0.844 / Rpim(I) all: 0.305 / Rrim(I) all: 0.763 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XDSdata scaling
MOLREP7.0.077phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2UY2

2uy2


Resolution: 1.12→46.89 Å / Cor.coef. Fo:Fc: 0.982 / Cor.coef. Fo:Fc free: 0.978 / SU B: 0.407 / SU ML: 0.019 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.027 / ESU R Free: 0.028 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1604 6420 5 %RANDOM
Rwork0.1497 ---
obs0.1502 120942 99.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 57.74 Å2 / Biso mean: 16.648 Å2 / Biso min: 9.91 Å2
Baniso -1Baniso -2Baniso -3
1--0.3 Å2-0 Å20 Å2
2---0.53 Å20 Å2
3---0.83 Å2
Refinement stepCycle: final / Resolution: 1.12→46.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2300 0 27 371 2698
Biso mean--29.41 32.45 -
Num. residues----303
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0122497
X-RAY DIFFRACTIONr_bond_other_d0.0020.0182222
X-RAY DIFFRACTIONr_angle_refined_deg1.4661.6363427
X-RAY DIFFRACTIONr_angle_other_deg1.6261.5765119
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2645333
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.00124.56125
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.16915355
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.674157
X-RAY DIFFRACTIONr_chiral_restr0.0780.2325
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023025
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02641
LS refinement shellResolution: 1.12→1.149 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.236 491 -
Rwork0.234 8844 -
all-9335 -
obs--99.91 %

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