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- PDB-8ose: C. perfringens chitinase CP4_3455 in complex with inhibitor bisdi... -

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Basic information

Entry
Database: PDB / ID: 8ose
TitleC. perfringens chitinase CP4_3455 in complex with inhibitor bisdionin C
ComponentsChitodextrinase
KeywordsHYDROLASE / chitinase / inhibitor / TIM barrel / necrotic enteritis
Function / homology
Function and homology information


chitin catabolic process / chitin binding / polysaccharide binding / hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate metabolic process
Similarity search - Function
Chitinase, C-terminal / Chitinase C / Immunoglobulin-like - #290 / CBM2, carbohydrate-binding domain superfamily / CBM2/CBM3, carbohydrate-binding domain superfamily / Glycosyl hydrolases family 18 (GH18) active site / Glycosyl hydrolases family 18 (GH18) active site signature. / : / Chitinase insertion domain superfamily / Chitinase II ...Chitinase, C-terminal / Chitinase C / Immunoglobulin-like - #290 / CBM2, carbohydrate-binding domain superfamily / CBM2/CBM3, carbohydrate-binding domain superfamily / 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. / Glycosyl hydrolases family 18 / Glycoside hydrolase family 18, catalytic domain / Glycoside hydrolase superfamily / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Chem-DW0 / Chitodextrinase
Similarity search - Component
Biological speciesClostridium perfringens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å
AuthorsBloch, Y. / Savvides, S.N.
Funding support Belgium, 1items
OrganizationGrant numberCountry
Research Foundation - Flanders (FWO)12S0519N Belgium
CitationJournal: Plos Pathog. / Year: 2024
Title: Clostridium perfringens chitinases, key enzymes during early stages of necrotic enteritis in broiler chickens.
Authors: Dierick, E. / Callens, C. / Bloch, Y. / Savvides, S.N. / Hark, S. / Pelzer, S. / Ducatelle, R. / Van Immerseel, F. / Goossens, E.
History
DepositionApr 18, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 12, 2023Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.2Nov 13, 2024Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _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 / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Chitodextrinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,7134
Polymers65,1731
Non-polymers5413
Water11,403633
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area520 Å2
ΔGint7 kcal/mol
Surface area22970 Å2
Unit cell
Length a, b, c (Å)50.329, 108.802, 111.080
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Chitodextrinase


Mass: 65172.504 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Residues [1-2 (MG)] cloning scar. Residues [569-575 (SHHHHHH)] purification tag.
Source: (gene. exp.) Clostridium perfringens (bacteria) / Gene: CP4_3455 / Plasmid: pET15 / Production host: Escherichia coli (E. coli) / Strain (production host): T7 Express lysY/Iq / References: UniProt: F8UNI5
#2: Chemical ChemComp-DW0 / 1,1'-PROPANE-1,3-DIYLBIS(3,7-DIMETHYL-3,7-DIHYDRO-1H-PURINE-2,6-DIONE) / BISDIONIN C / 1-[3-(3,7-DIMETHYL-2,6-DIOXO-2,3,6,7-TETRAHYDRO-1H-PURIN-1-YL)PROPYL]-3,7-DIMETHYL-2,3,6,7-TETRAHYDRO-1H-PURINE-2,6-DION E


Mass: 400.392 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H20N8O4
#3: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Feature type: SUBJECT OF INVESTIGATION / Comment: DMSO, precipitant*YM
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 633 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.33 Å3/Da / Density % sol: 47.28 %
Crystal growTemperature: 287 K / Method: vapor diffusion, hanging drop / pH: 7.9
Details: 0.2 M Lithium acetate dihydrate, 20% w/v Polyethylene glycol 3,350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 1.0332 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 30, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.35→49.47 Å / Num. obs: 133165 / % possible obs: 99.1 % / Redundancy: 5.78 % / Biso Wilson estimate: 17.24 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.044 / Net I/σ(I): 18.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
6.04-49.475.0643.5216090.9980.0395.5
1.35-1.395.452.3896410.7390.84498.1

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDS20180126data reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.35→49.47 Å / SU ML: 0.1055 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 14.1431
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.163 1989 1.49 %
Rwork0.1386 131174 -
obs0.1389 133163 99.09 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 24.65 Å2
Refinement stepCycle: LAST / Resolution: 1.35→49.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4470 0 37 633 5140
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.014789
X-RAY DIFFRACTIONf_angle_d1.11516547
X-RAY DIFFRACTIONf_chiral_restr0.0862687
X-RAY DIFFRACTIONf_plane_restr0.0099902
X-RAY DIFFRACTIONf_dihedral_angle_d11.83471761
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.35-1.380.24111360.19839145X-RAY DIFFRACTION98.05
1.38-1.420.19161430.16849330X-RAY DIFFRACTION99.67
1.42-1.460.17571490.15359326X-RAY DIFFRACTION99.91
1.46-1.510.17741380.13289365X-RAY DIFFRACTION99.78
1.51-1.560.18381380.12459361X-RAY DIFFRACTION99.75
1.56-1.630.14961410.11419360X-RAY DIFFRACTION99.67
1.63-1.70.13321460.10879337X-RAY DIFFRACTION99.75
1.7-1.790.14531450.11379421X-RAY DIFFRACTION99.6
1.79-1.90.16831410.12269320X-RAY DIFFRACTION99.38
1.9-2.050.12881430.12349376X-RAY DIFFRACTION99.21
2.05-2.260.13971390.12239371X-RAY DIFFRACTION98.83
2.26-2.580.15641420.13459378X-RAY DIFFRACTION98.59
2.58-3.250.17781440.15089430X-RAY DIFFRACTION98.23
3.25-49.470.17181440.15019654X-RAY DIFFRACTION97.05
Refinement TLS params.Method: refined / Origin x: 11.342 Å / Origin y: 1.746 Å / Origin z: 5.512 Å
111213212223313233
T0.199697701356 Å20.0177169641787 Å20.0328882398155 Å2-0.204358723235 Å20.0396195864557 Å2--0.251179547205 Å2
L0.146979780922 °2-0.14249822388 °2-0.114376177196 °2-0.238879763043 °20.154814488796 °2--0.166355108237 °2
S-0.0661821444758 Å °-0.0789286457081 Å °0.327932167825 Å °0.367561246676 Å °0.403186869613 Å °0.161751492907 Å °0.248223490043 Å °-0.27989453899 Å °0.00669752443578 Å °
Refinement TLS groupSelection details: ( CHAIN A AND RESID 701:701 )

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