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- PDB-6yn4: Structure of D169A/E171A double mutant of chitinase Chit42 from T... -

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Basic information

Entry
Database: PDB / ID: 6yn4
TitleStructure of D169A/E171A double mutant of chitinase Chit42 from Trichoderma harzianum complexed with chitintetraose.
ComponentsEndochitinase 42
KeywordsHYDROLASE / CHITINASE / HYDROLYTIC ENZYME / GLYCOSIL HYDROLASE / CHITIN / N-ACETYLGLUCOSAMINE / CHITINTETRAOSE / TETRAACETYL-CHITOTETRAOSE / COMPLEX / PREBIOTIC / OLIGOSACCHARIDE / CHITOOLOGOSACCHARIDE / TRICHODERMA HARZIANUM
Function / homology
Function and homology information


chitinase / chitinase activity / chitin catabolic process / chitin binding / polysaccharide catabolic process / extracellular region
Similarity search - Function
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. / Glycoside hydrolase family 18, catalytic domain / Glycosyl hydrolases family 18 / Glycoside hydrolase superfamily
Similarity search - Domain/homology
ACETATE ION / DI(HYDROXYETHYL)ETHER / Endochitinase 42
Similarity search - Component
Biological speciesTrichoderma harzianum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.82 Å
AuthorsJimenez-Ortega, E. / Sanz-Aparicio, J.
CitationJournal: Comput Struct Biotechnol J / Year: 2021
Title: Structural inspection and protein motions modelling of a fungal glycoside hydrolase family 18 chitinase by crystallography depicts a dynamic enzymatic mechanism
Authors: Jimenez-Ortega, E. / Kidibule, P.E. / Fernandez-Lobato, M. / Sanz-Aparicio, J.
History
DepositionApr 10, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 20, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Endochitinase 42
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,10515
Polymers45,9681
Non-polymers2,13714
Water7,044391
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4820 Å2
ΔGint-106 kcal/mol
Surface area14380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.352, 68.352, 177.757
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Endochitinase 42 / 42 kDa endochitinase / Chitinase 42


Mass: 45968.234 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trichoderma harzianum (fungus) / Gene: chit42 / Plasmid: pBluescript SK (+) / Production host: Komagataella phaffii GS115 (fungus) / References: UniProt: P48827, chitinase

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Sugars , 2 types, 2 molecules

#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: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE

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Non-polymers , 4 types, 403 molecules

#4: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Zn
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 391 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.47 Å3/Da / Density % sol: 50.27 % / Description: Bar
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 15 PEG 3000, 0.2 M Zinc Acetate, 0.1 M imidazole pH 8, 3% MPD Co-crystallization 2mM EDTA, 20mM chitintetraose. Cryoprotectant mother liquor supplemented with 20% PEG 400, 5 mM chitintetraose, 2 mM EDTA.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97924 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 28, 2018 / Details: KB focusing mirrors
RadiationMonochromator: Si(111) channel-cut, cryocooled / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97924 Å / Relative weight: 1
ReflectionResolution: 1.82→48.38 Å / Num. obs: 38716 / % possible obs: 99.9 % / Redundancy: 6.5 % / CC1/2: 0.997 / Rmerge(I) obs: 0.107 / Rpim(I) all: 0.045 / Rrim(I) all: 0.117 / Net I/σ(I): 14.2
Reflection shellResolution: 1.82→1.86 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.701 / Mean I/σ(I) obs: 4.8 / Num. unique obs: 2258 / CC1/2: 0.917 / Rpim(I) all: 0.286 / Rrim(I) all: 0.758 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0257refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
Aimless7.0.057data scaling
MOLREP7.0.077phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6EPB

6epb


Resolution: 1.82→48.38 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.935 / SU B: 2.668 / SU ML: 0.082 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.133 / ESU R Free: 0.122 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2113 1987 5.1 %RANDOM
Rwork0.1797 ---
obs0.1813 36690 99.76 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 52.82 Å2 / Biso mean: 15.511 Å2 / Biso min: 6.13 Å2
Baniso -1Baniso -2Baniso -3
1-0.58 Å20 Å20 Å2
2--0.58 Å20 Å2
3----1.15 Å2
Refinement stepCycle: final / Resolution: 1.82→48.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2994 0 128 393 3515
Biso mean--30.29 27.29 -
Num. residues----389
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0133254
X-RAY DIFFRACTIONr_bond_other_d0.0090.0172846
X-RAY DIFFRACTIONr_angle_refined_deg1.4781.6754441
X-RAY DIFFRACTIONr_angle_other_deg1.5651.6126635
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4525406
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.61724.295149
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.74815470
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.165157
X-RAY DIFFRACTIONr_chiral_restr0.0750.2437
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023690
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02685
LS refinement shellResolution: 1.82→1.867 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.254 138 -
Rwork0.219 2683 -
all-2821 -
obs--100 %

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