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

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Basic information

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


endochitinase activity / chitinase / 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 / Glycosyl hydrolases family 18 (GH18) domain profile. / Glycoside hydrolase family 18, catalytic domain / Glycoside hydrolase superfamily
Similarity search - Domain/homology
ACETATE ION / Endochitinase 42
Similarity search - Component
Biological speciesTrichoderma harzianum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 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 7, 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)47,5798
Polymers45,9681
Non-polymers1,6117
Water7,746430
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3820 Å2
ΔGint-48 kcal/mol
Surface area14190 Å2
Unit cell
Length a, b, c (Å)68.160, 68.160, 178.864
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

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


Type: oligosaccharide / Mass: 1237.172 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-4DGlcpNAcb1-4DGlcpNAcb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,6,5/[a2122h-1b_1-5_2*NCC/3=O]/1-1-1-1-1-1/a4-b1_b4-c1_c4-d1_d4-e1_e4-f1WURCSPDB2Glycan 1.1.0
[][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}}}}LINUCSPDB-CARE
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 430 / Source method: isolated from a natural source / Formula: H2O
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: 50.3 % / Description: Bar
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 19% PEG 3000, 0.1M Zinc acetate, 0.1M Zinc chloride, 0.1M imidazole pH8. Soaking 30mM chitinhexaose.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 19, 2018 / Details: KB Mirrors
RadiationMonochromator: Si(111) channel-cut, cryocooled / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.75→48.24 Å / Num. obs: 43306 / % possible obs: 99.7 % / Redundancy: 7.3 % / CC1/2: 0.998 / Rmerge(I) obs: 0.082 / Rpim(I) all: 0.032 / Rrim(I) all: 0.088 / Net I/σ(I): 16.9
Reflection shellResolution: 1.75→1.78 Å / Redundancy: 7 % / Rmerge(I) obs: 0.678 / Mean I/σ(I) obs: 3.7 / Num. unique obs: 2325 / CC1/2: 0.873 / Rpim(I) all: 0.27 / Rrim(I) all: 0.732 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0257refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
Aimless7.0.066data scaling
MOLREP7.0.066phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6EPB

6epb


Resolution: 1.75→48.24 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.948 / SU B: 4.15 / SU ML: 0.071 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.106 / ESU R Free: 0.103
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1964 2142 4.9 %RANDOM
Rwork0.1637 ---
obs0.1653 41133 99.49 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 67.64 Å2 / Biso mean: 22.109 Å2 / Biso min: 9.32 Å2
Baniso -1Baniso -2Baniso -3
1-0.33 Å20 Å20 Å2
2--0.33 Å20 Å2
3----0.65 Å2
Refinement stepCycle: final / Resolution: 1.75→48.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2994 0 100 431 3525
Biso mean--27.21 30.39 -
Num. residues----389
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0133216
X-RAY DIFFRACTIONr_bond_other_d0.0120.0172803
X-RAY DIFFRACTIONr_angle_refined_deg1.4891.6774394
X-RAY DIFFRACTIONr_angle_other_deg1.6291.6146533
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1835400
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.00124.257148
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.27715469
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.977157
X-RAY DIFFRACTIONr_chiral_restr0.0740.2434
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023654
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02681
LS refinement shellResolution: 1.75→1.795 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.242 141 -
Rwork0.218 2996 -
all-3137 -
obs--99.87 %
Refinement TLS params.Method: refined / Origin x: -29.0631 Å / Origin y: -0.4917 Å / Origin z: -23.1581 Å
111213212223313233
T0.0193 Å2-0.01 Å2-0.0012 Å2-0.0052 Å20.0017 Å2--0.02 Å2
L0.0928 °20.0987 °20.1018 °2-0.1297 °20.1138 °2--0.4112 °2
S-0.0314 Å °0.0133 Å °-0.0032 Å °-0.0282 Å °0.0112 Å °0.0177 Å °-0.0856 Å °0.0456 Å °0.0202 Å °

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