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- PDB-8c6z: necrotic enteritis associated Clostridium p. chitinase F8UNI4 in ... -

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Basic information

Entry
Database: PDB / ID: 8c6z
Titlenecrotic enteritis associated Clostridium p. chitinase F8UNI4 in complex with inhibitor bisdionin C
ComponentsChitinase B
KeywordsHYDROLASE / GH18 / enzyme / inhibitor / chitinase
Function / homology
Function and homology information


chitinase / chitin catabolic process / chitin binding / carbohydrate metabolic process / hydrolase activity
Similarity search - Function
: / 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
: / : / Chem-DW0 / chitinase
Similarity search - Component
Biological speciesClostridium perfringens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsBloch, Y. / Savvides, S.N.
Funding support Belgium, 1items
OrganizationGrant numberCountry
Research Foundation - Flanders (FWO) 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
DepositionJan 12, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 31, 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: Chitinase B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,5696
Polymers69,4841
Non-polymers1,0855
Water7,494416
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: light scattering, monomer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area320 Å2
ΔGint-24 kcal/mol
Surface area22560 Å2
Unit cell
Length a, b, c (Å)67.401, 67.401, 355.823
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 Chitinase B / Glycosyl hydrolase


Mass: 69484.242 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Residues 600 onwards stem from the vector. Residues [608-621] V5 epitope tag. Residues [625-630] 6His tag.
Source: (gene. exp.) Clostridium perfringens (bacteria) / Gene: CP4_3454, pNetB_00069 / Plasmid: pBAD TOPO TA / Production host: Escherichia coli (E. coli) / Strain (production host): Top10 / References: UniProt: F8UNI4
#2: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Co
#3: Chemical ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cd
#4: 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.: 2 / Source method: obtained synthetically / Formula: C17H20N8O4 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 416 / 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: 2.91 Å3/Da / Density % sol: 57.7 %
Crystal growTemperature: 287 K / Method: vapor diffusion, sitting drop
Details: 5mM CoCl2,5mM NiCl2,5 mM CdCl2, 5mM MgCl2,100mM HEPES pH7.5, 12% PEG 3350. Cryoprotected with 20% ethylene glycol prior to vitrification.

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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: May 5, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.85→58.6 Å / Num. obs: 70266 / % possible obs: 98 % / Redundancy: 6.8 % / Biso Wilson estimate: 38.48 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.1 / Net I/σ(I): 12.61
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
5.53-58.66.441.3228390.9990.04193.7
3.92-5.536.7639.9348330.9990.04495.4
3.2-3.926.931.5861890.9980.05796.9
2.77-3.26.719.0873300.9930.09697.7
2.48-2.776.8711.4182100.9790.17197.9
2.27-2.486.927.1391000.9440.27598.5
2.1-2.276.844.3498790.8580.44598.8
1.96-2.16.812.41106300.6690.77499.3
1.85-1.966.811.2112560.3561.41399.1

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDS20180126data reduction
PHASER2.8.1phasing
XDS20180126data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: F8UNI5

Resolution: 1.85→48.94 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 22.77 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2234 2103 2.99 %
Rwork0.1965 68153 -
obs0.1973 70256 98.02 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 87.77 Å2 / Biso mean: 39.8644 Å2 / Biso min: 22.17 Å2
Refinement stepCycle: final / Resolution: 1.85→48.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4442 0 60 416 4918
Biso mean--61.32 42.74 -
Num. residues----574
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.85-1.890.35171380.34894475461399
1.89-1.940.35841400.30544531467199
1.94-1.990.28791400.27934524466499
1.99-2.050.28891390.2624492463199
2.05-2.120.29681380.25494531466999
2.12-2.190.30641400.23234504464499
2.19-2.280.24751370.21674514465199
2.28-2.390.25081420.20834528467099
2.39-2.510.26741380.2134540467898
2.51-2.670.23561380.20384487462598
2.67-2.870.24491410.20254523466498
2.88-3.160.23221400.19524553469398
3.16-3.620.22371380.19354573471197
3.62-4.560.16121460.16474596474296
4.56-48.940.18631480.16154782493094
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.17890.59070.05941.0404-0.26050.6371-0.13640.00350.084-0.11910.0029-0.0369-0.01650.023-00.25190.0135-0.04150.33880.02170.2519-3.3376-9.561626.5747
20.0054-0.01850.01470.1136-0.08140.06030.0050.02360.0203-0.00680.0253-0.0119-0.00630.01150.00020.3909-0.0196-0.06090.56990.05510.42978.0809-5.031730.1437
30.00810.017-0.00740.0388-0.01630.0074-0.00740.01250.0099-0.00920.0027-0.0046-0.02790.0196-0.00010.9875-0.00990.09191.11250.01921.182114.95493.166724.6509
Refinement TLS groupSelection details: chain A

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