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- PDB-9hj7: Structure of Chitinase 35 from Metschnikowia pulcherrima (MpChit35) -

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Basic information

Entry
Database: PDB / ID: 9hj7
TitleStructure of Chitinase 35 from Metschnikowia pulcherrima (MpChit35)
ComponentsChitinase
KeywordsHYDROLASE / Chitinase / exochitinase
Function / homology
Function and homology information


endochitinase activity / carbohydrate metabolic process / extracellular region
Similarity search - Function
Chitinase Cts1-like / : / 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 / Chitinase
Similarity search - Component
Biological speciesMetschnikowia pulcherrima (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å
AuthorsFernandez-Garcia, A. / Sanz-Aparicio, J.
Funding support Spain, 2items
OrganizationGrant numberCountry
Spanish Ministry of Science, Innovation, and UniversitiesPID2019-105838RB-C33 Spain
Spanish Ministry of Science, Innovation, and UniversitiesPID2022-136367OB-C33 Spain
CitationJournal: Int.J.Biol.Macromol. / Year: 2025
Title: Structural-mechanistic insights and performance engineering of chitinase MpChit35 for tailored chito-oligosaccharide production.
Authors: Minguet-Lobato, M. / Fernandez-Garcia, A. / Jimenez-Ortega, E. / Cervantes, F.V. / Sanchez-Pozo, P. / Plou, F.J. / Sanz-Aparicio, J. / Fernandez-Lobato, M.
History
DepositionNov 28, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 27, 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: Chitinase
B: Chitinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,39013
Polymers64,1802
Non-polymers1,21011
Water2,720151
1
A: Chitinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,5686
Polymers32,0901
Non-polymers4785
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Chitinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,8227
Polymers32,0901
Non-polymers7326
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.582, 54.850, 97.776
Angle α, β, γ (deg.)90.00, 107.72, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein / Sugars , 2 types, 3 molecules AB

#1: Protein Chitinase


Mass: 32089.826 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Metschnikowia pulcherrima (fungus) / Gene: MPUL0D06620, METSCH_D06620 / Production host: Komagataella phaffii GS115 (fungus) / References: UniProt: A0A4P6XUI5
#5: 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.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
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

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Non-polymers , 4 types, 161 molecules

#2: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


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


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 151 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.16 Å3/Da / Density % sol: 43.16 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 22% PEG 4000, 100mM magnesium chloride, 100mM sodium acetate pH 4.6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 28, 2023 / Details: KB MIRRORS
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.55→47.31 Å / Num. obs: 20240 / % possible obs: 99.5 % / Redundancy: 6.1 % / CC1/2: 0.985 / Rmerge(I) obs: 0.184 / Rpim(I) all: 0.08 / Rrim(I) all: 0.201 / Χ2: 1.42 / Net I/σ(I): 7.5
Reflection shellResolution: 2.55→2.66 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.474 / Mean I/σ(I) obs: 4.7 / Num. unique obs: 2416 / CC1/2: 0.915 / Rpim(I) all: 0.213 / Rrim(I) all: 0.521 / Χ2: 1.94 / % possible all: 97.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
XDSdata reduction
XDSdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.55→47.31 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.892 / SU B: 9.904 / SU ML: 0.213 / Cross valid method: THROUGHOUT / ESU R: 3.998 / ESU R Free: 0.309 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23817 976 4.9 %RANDOM
Rwork0.18108 ---
obs0.18386 19134 98.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.923 Å2
Baniso -1Baniso -2Baniso -3
1--1.15 Å2-0 Å2-2.04 Å2
2--0.03 Å2-0 Å2
3---2.01 Å2
Refinement stepCycle: 1 / Resolution: 2.55→47.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4560 0 29 151 4740
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0124730
X-RAY DIFFRACTIONr_bond_other_d0.0010.0164248
X-RAY DIFFRACTIONr_angle_refined_deg1.4361.7966413
X-RAY DIFFRACTIONr_angle_other_deg0.491.7499799
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8165592
X-RAY DIFFRACTIONr_dihedral_angle_2_deg6.735520
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.00910716
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0660.2671
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.025653
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021135
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_it1.7532.3762338
X-RAY DIFFRACTIONr_mcbond_other1.7472.3762338
X-RAY DIFFRACTIONr_mcangle_it2.8554.2622922
X-RAY DIFFRACTIONr_mcangle_other2.8544.2652923
X-RAY DIFFRACTIONr_scbond_it2.5422.7382392
X-RAY DIFFRACTIONr_scbond_other2.5412.7392393
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.1354.863486
X-RAY DIFFRACTIONr_long_range_B_refined6.78524.495271
X-RAY DIFFRACTIONr_long_range_B_other6.78424.55272
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.55→2.611 Å
RfactorNum. reflection% reflection
Rfree0.244 63 -
Rwork0.272 1365 -
obs--94.07 %

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