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- PDB-6epb: Structure of Chitinase 42 from Trichoderma harzianum -

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Basic information

Entry
Database: PDB / ID: 6epb
TitleStructure of Chitinase 42 from Trichoderma harzianum
ComponentsEndochitinase 42
KeywordsHYDROLASE / Carbohydrates / Catalysis / Catalytic Domain / Cloning / Glycoside Hydrolases / Fungal Proteins / Transglycosilation / Chitinase.
Function / homology
Function and homology information


chitinase / chitinase activity / chitin catabolic process / chitin binding / polysaccharide catabolic process / extracellular region
Similarity search - Function
Chitinase A; domain 3 - #10 / 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 / Chitinase A; domain 3 ...Chitinase A; domain 3 - #10 / 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 / Chitinase A; domain 3 / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Roll / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / IMIDAZOLE / Endochitinase 42
Similarity search - Component
Biological speciesTrichoderma harzianum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsRamirez-Escudero, M. / Jimenez-Ortega, E. / Sanz-Aparicio, J.
CitationJournal: Microb. Cell Fact. / Year: 2018
Title: Use of chitin and chitosan to produce new chitooligosaccharides by chitinase Chit42: enzymatic activity and structural basis of protein specificity.
Authors: Kidibule, P.E. / Santos-Moriano, P. / Jimenez-Ortega, E. / Ramirez-Escudero, M. / Limon, M.C. / Remacha, M. / Plou, F.J. / Sanz-Aparicio, J. / Fernandez-Lobato, M.
History
DepositionOct 11, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 26, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 23, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _citation.country / _database_2.pdbx_DOI ..._citation.country / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Endochitinase 42
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,07533
Polymers46,0701
Non-polymers2,00432
Water5,621312
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5680 Å2
ΔGint-161 kcal/mol
Surface area14630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.353, 68.353, 178.279
Angle α, β, γ (deg.)90.00, 90.00, 90.00
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: 46070.281 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trichoderma harzianum (fungus) / Gene: chit42 / Production host: Komagataella phaffii GS115 (fungus) / References: UniProt: P48827, chitinase

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Non-polymers , 5 types, 344 molecules

#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 312 / Source method: isolated from a natural source / Formula: H2O

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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: 2.26 Å3/Da / Density % sol: 45.58 % / Description: Bar: square transversal section
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 22% PEG 3000, 0.1 M Imidazole pH 8, 0.2 M Zinc acetate. Cryoprotectant mother liquor supplemented with 20 % ethylene glycol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97929 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Oct 13, 2016 / Details: KB focusing mirrors
RadiationMonochromator: Si(111) channel-cut, cryocooled / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97929 Å / Relative weight: 1
ReflectionResolution: 1.75→68.35 Å / Num. obs: 43534 / % possible obs: 99.8 % / Redundancy: 6.4 % / Biso Wilson estimate: 14.536 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.074 / Rpim(I) all: 0.032 / Rrim(I) all: 0.081 / Net I/σ(I): 16.9
Reflection shellResolution: 1.75→1.78 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.601 / Mean I/σ(I) obs: 3.6 / Num. unique obs: 2325 / CC1/2: 0.867 / Rpim(I) all: 0.249 / Rrim(I) all: 0.651 / % possible all: 99.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDS0.52data reduction
Aimless7.0.029data scaling
MOLREP7.0.029phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3G6L

3g6l


Resolution: 1.75→63.82 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.94 / SU B: 2.132 / SU ML: 0.069 / Cross valid method: THROUGHOUT / ESU R: 0.116 / ESU R Free: 0.113 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21908 2229 5.1 %RANDOM
Rwork0.18387 ---
obs0.18563 41239 99.68 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.915 Å2
Baniso -1Baniso -2Baniso -3
1-0.37 Å20 Å20 Å2
2--0.37 Å20 Å2
3----0.73 Å2
Refinement stepCycle: 1 / Resolution: 1.75→63.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3001 0 108 312 3421
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.023193
X-RAY DIFFRACTIONr_bond_other_d0.0020.022829
X-RAY DIFFRACTIONr_angle_refined_deg1.3081.9474307
X-RAY DIFFRACTIONr_angle_other_deg0.92236567
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.015398
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.61725.172145
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.0115469
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.934157
X-RAY DIFFRACTIONr_chiral_restr0.0820.2451
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023611
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02662
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_it1.051.8951578
X-RAY DIFFRACTIONr_mcbond_other1.0461.8881573
X-RAY DIFFRACTIONr_mcangle_it1.6962.8291972
X-RAY DIFFRACTIONr_mcangle_other1.6972.831973
X-RAY DIFFRACTIONr_scbond_it1.1982.071615
X-RAY DIFFRACTIONr_scbond_other1.1972.0721616
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.8413.0182334
X-RAY DIFFRACTIONr_long_range_B_refined4.53423.3033729
X-RAY DIFFRACTIONr_long_range_B_other4.53323.3053730
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.75→1.795 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.286 180 -
Rwork0.234 2962 -
obs--99.12 %

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