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- PDB-8owf: Clostridium perfringens chitinase CP4_3455 with chitosan -

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Basic information

Entry
Database: PDB / ID: 8owf
TitleClostridium perfringens chitinase CP4_3455 with chitosan
ComponentsChitodextrinase
KeywordsHYDROLASE / chitinase / necrotic enteritis / TIM barrel / inhibitor
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
Biological speciesClostridium perfringens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsBloch, Y. / Savvides, S.N.
Funding support Belgium, 1items
OrganizationGrant numberCountry
Research Foundation - Flanders (FWO)12S0519N Belgium
Citation
Journal: 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.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2012
Title: Towards automated crystallographic structure refinement with phenix.refine.
Authors: Afonine, P.V. / Grosse-Kunstleve, R.W. / Echols, N. / Headd, J.J. / Moriarty, N.W. / Mustyakimov, M. / Terwilliger, T.C. / Urzhumtsev, A. / Zwart, P.H. / Adams, P.D.
#2: Journal: Acta Crystallogr D Struct Biol / Year: 2019
Title: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix.
Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty ...Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty / Robert D Oeffner / Billy K Poon / Michael G Prisant / Randy J Read / Jane S Richardson / David C Richardson / Massimo D Sammito / Oleg V Sobolev / Duncan H Stockwell / Thomas C Terwilliger / Alexandre G Urzhumtsev / Lizbeth L Videau / Christopher J Williams / Paul D Adams /
Abstract: Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological ...Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological processes and to develop new therapeutics against diseases. The overall structure-solution workflow is similar for these techniques, but nuances exist because the properties of the reduced experimental data are different. Software tools for structure determination should therefore be tailored for each method. Phenix is a comprehensive software package for macromolecular structure determination that handles data from any of these techniques. Tasks performed with Phenix include data-quality assessment, map improvement, model building, the validation/rebuilding/refinement cycle and deposition. Each tool caters to the type of experimental data. The design of Phenix emphasizes the automation of procedures, where possible, to minimize repetitive and time-consuming manual tasks, while default parameters are chosen to encourage best practice. A graphical user interface provides access to many command-line features of Phenix and streamlines the transition between programs, project tracking and re-running of previous tasks.
History
DepositionApr 27, 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)66,2714
Polymers65,1731
Non-polymers1,0993
Water12,358686
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2590 Å2
ΔGint8 kcal/mol
Surface area22760 Å2
Unit cell
Length a, b, c (Å)50.436, 108.498, 111.407
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 [569-575] encode a cloning scar and purification tag which weren't removed. Trimmed construct compared to WT protein.
Source: (gene. exp.) Clostridium perfringens (bacteria) / Gene: CP4_3455 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): T7 Express lysY/Iq / References: UniProt: F8UNI5
#2: Polysaccharide 2-amino-2-deoxy-beta-D-glucopyranose-(1-4)-2-amino-2-deoxy-beta-D-glucopyranose-(1-4)-2-amino-2- ...2-amino-2-deoxy-beta-D-glucopyranose-(1-4)-2-amino-2-deoxy-beta-D-glucopyranose-(1-4)-2-amino-2-deoxy-beta-D-glucopyranose-(1-4)-2-amino-2-deoxy-beta-D-glucopyranose-(1-4)-2-amino-2-deoxy-beta-D-glucopyranose-(1-4)-2-amino-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 984.950 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNb1-4DGlcpNb1-4DGlcpNb1-4DGlcpNb1-4DGlcpNb1-4DGlcpNb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,6,5/[a2122h-1b_1-5_2*N]/1-1-1-1-1-1/a4-b1_b4-c1_c4-d1_d4-e1_e4-f1WURCSPDB2Glycan 1.1.0
[][b-D-GlcpN]{[(4+1)][b-D-GlcpN]{[(4+1)][b-D-GlcpN]{[(4+1)][b-D-GlcpN]{[(4+1)][b-D-GlcpN]{[(4+1)][b-D-GlcpN]{}}}}}}LINUCSPDB-CARE
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 686 / 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: 2.34 Å3/Da / Density % sol: 47.4 %
Crystal growTemperature: 287 K / Method: vapor diffusion, sitting drop
Details: PEGION A4: 0.2 M Lithium chloride, 20% w/v Polyethylene glycol 3,350, 1mM chitosan hexamer

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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: 0.97625 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 27, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.3→45.74 Å / Num. obs: 148328 / % possible obs: 98.5 % / Redundancy: 3.77 % / Biso Wilson estimate: 15.71 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.055 / Net I/σ(I): 14.07
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
3.89-45.743.8758.6257000.9990.02395
1.38-1.473.822.22225860.7150.74799.5
1.3-1.383.311.31231940.451.15596.5

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDS20180126data reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.3→45.74 Å / SU ML: 0.1314 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.073
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1698 2008 1.35 %
Rwork0.1451 146309 -
obs0.1455 148317 98.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 23.86 Å2
Refinement stepCycle: LAST / Resolution: 1.3→45.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4468 0 72 686 5226
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00594713
X-RAY DIFFRACTIONf_angle_d0.85116421
X-RAY DIFFRACTIONf_chiral_restr0.0754701
X-RAY DIFFRACTIONf_plane_restr0.0072829
X-RAY DIFFRACTIONf_dihedral_angle_d15.8711708
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3-1.330.27371410.26569773X-RAY DIFFRACTION93.4
1.33-1.370.27751430.247110346X-RAY DIFFRACTION98.79
1.37-1.410.27961380.233110495X-RAY DIFFRACTION99.62
1.41-1.450.24941570.216110413X-RAY DIFFRACTION99.47
1.45-1.510.21681380.177810475X-RAY DIFFRACTION99.63
1.51-1.570.19421440.151310458X-RAY DIFFRACTION99.38
1.57-1.640.1791420.136610503X-RAY DIFFRACTION99.54
1.64-1.720.16541460.132910519X-RAY DIFFRACTION99.74
1.72-1.830.16471400.12610508X-RAY DIFFRACTION99.4
1.83-1.970.14221410.12210549X-RAY DIFFRACTION99.42
1.97-2.170.13431440.120210518X-RAY DIFFRACTION98.98
2.17-2.490.12741470.122310549X-RAY DIFFRACTION99.06
2.49-3.130.19171440.14210596X-RAY DIFFRACTION98.23
3.13-45.740.1621430.14910607X-RAY DIFFRACTION95.49

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