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- PDB-7zy9: Structure of D165A/D167A double mutant of Chit33 from Trichoderma... -

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Basic information

Entry
Database: PDB / ID: 7zy9
TitleStructure of D165A/D167A double mutant of Chit33 from Trichoderma harzianum complexed with chitintetraose.
ComponentsEndochitinase 33
KeywordsHYDROLASE / Chitinase / endo-chitinase / glycoside hydrolase / fungal chitinase / Thichoderma harzianum / GH18 family / chitooligosaccharide / oligosaccharide / COS / chitin / chitosan / chitintetraose.
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
Biological speciesTrichoderma harzianum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 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)33,3432
Polymers32,5121
Non-polymers8311
Water5,423301
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)65.421, 66.776, 76.445
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: 32511.906 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: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 830.786 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,4,3/[a2122h-1b_1-5_2*NCC/3=O]/1-1-1-1/a4-b1_b4-c1_c4-d1WURCSPDB2Glycan 1.1.0
[][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 301 / 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: 2.53 Å3/Da / Density % sol: 51.41 % / Description: Prism bar shape
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 30% PEG 1500, 20% glycerol. Soaking conditions: 32% PEG 1500, 18% glycerol, 18 mM chitintetraose.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97918 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 22, 2018 / Details: KB Mirrors
RadiationMonochromator: Si(111) channel-cut, cryocooled / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.6→46.78 Å / Num. obs: 44920 / % possible obs: 100 % / Redundancy: 6.6 % / CC1/2: 0.997 / Rmerge(I) obs: 0.083 / Rpim(I) all: 0.035 / Rrim(I) all: 0.09 / Net I/σ(I): 12.8
Reflection shellResolution: 1.6→1.63 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.623 / Mean I/σ(I) obs: 3.1 / Num. unique obs: 2190 / CC1/2: 0.883 / Rpim(I) all: 0.255 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XDSdata scaling
MOLREP7.0.038phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2UY2

2uy2


Resolution: 1.6→46.78 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.967 / SU B: 1.305 / SU ML: 0.046 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.07 / ESU R Free: 0.069 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1684 2229 5 %RANDOM
Rwork0.1477 ---
obs0.1487 42630 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 56.51 Å2 / Biso mean: 18.041 Å2 / Biso min: 8.5 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å2-0 Å20 Å2
2---0.01 Å20 Å2
3---0.02 Å2
Refinement stepCycle: final / Resolution: 1.6→46.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2292 0 57 302 2651
Biso mean--39.7 34.4 -
Num. residues----303
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0132490
X-RAY DIFFRACTIONr_bond_other_d0.0050.0152198
X-RAY DIFFRACTIONr_angle_refined_deg1.4981.6683424
X-RAY DIFFRACTIONr_angle_other_deg1.81.6065072
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0365327
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.21824.667120
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.65315345
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.084156
X-RAY DIFFRACTIONr_chiral_restr0.0820.2339
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022984
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02636
LS refinement shellResolution: 1.6→1.642 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.18 160 -
Rwork0.196 3101 -
all-3261 -
obs--99.85 %

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