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- PDB-6jk9: Crystal structure of Serratia marcescens Chitinase B complexed wi... -

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Basic information

Entry
Database: PDB / ID: 6jk9
TitleCrystal structure of Serratia marcescens Chitinase B complexed with compound 2-8-14
ComponentsChitinase
KeywordsHYDROLASE / chitianse / Serratia marcescens / complex
Function / homology
Function and homology information


chitinase activity / endochitinase activity / chitinase / chitin catabolic process / chitin binding / polysaccharide catabolic process / carbohydrate binding / extracellular region
Similarity search - Function
Chitin-binding domain type 3 / Carbohydrate-binding module family 5/12 / Carbohydrate-binding module superfamily 5/12 / 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. ...Chitin-binding domain type 3 / Carbohydrate-binding module family 5/12 / Carbohydrate-binding module superfamily 5/12 / 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
Similarity search - Domain/homology
Chem-BU0 / Chitinase B / chitinase
Similarity search - Component
Biological speciesSerratia marcescens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.312 Å
AuthorsJiang, X. / Yang, Q.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China31425021 China
CitationJournal: J.Med.Chem. / Year: 2020
Title: A Series of Compounds Bearing a Dipyrido-Pyrimidine Scaffold Acting as Novel Human and Insect Pest Chitinase Inhibitors.
Authors: Jiang, X. / Kumar, A. / Motomura, Y. / Liu, T. / Zhou, Y. / Moro, K. / Zhang, K.Y.J. / Yang, Q.
History
DepositionFeb 27, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 19, 2020Provider: repository / Type: Initial release
Revision 1.1Feb 26, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.0Oct 9, 2024Group: Non-polymer description / Structure summary
Category: chem_comp / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp.formula

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Chitinase
B: Chitinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,3604
Polymers110,4572
Non-polymers9032
Water3,873215
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2860 Å2
ΔGint-11 kcal/mol
Surface area36810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.375, 103.667, 185.438
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Chitinase / SmChiB


Mass: 55228.664 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Serratia marcescens (bacteria) / Gene: chiB / Plasmid: pet28a / Production host: Escherichia coli K-12 (bacteria) / Strain (production host): K-12 / References: UniProt: Q54276, UniProt: P11797*PLUS
#2: Chemical ChemComp-BU0 / 6-azanyl-2-oxidanylidene-N-[(1S)-1-phenylethyl]-7-(phenylmethyl)-1$l^{4},9-diaza-7-azoniatricyclo[8.4.0.0^{3,8}]tetradeca-1(14),3(8),4,6,10,12-hexaene-5-carboxamide


Mass: 451.520 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H25N5O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 215 / Source method: isolated from a natural source / Formula: H2O
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: 2.41 Å3/Da / Density % sol: 48.95 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 50 mM citrate (pH 5.6), 0.5 M Li2SO4, 0.25 M (NH4)2SO4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NFPSS / Beamline: BL18U / Wavelength: 0.97778 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 20, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97778 Å / Relative weight: 1
ReflectionResolution: 2.312→30.162 Å / Num. obs: 47308 / % possible obs: 98.98 % / Redundancy: 12.8 % / Rsym value: 0.082 / Net I/σ(I): 35.5
Reflection shellResolution: 2.49→2.53 Å / Mean I/σ(I) obs: 4.45 / Num. unique obs: 1853 / Rsym value: 0.307 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4Z2G

4z2g


Resolution: 2.312→29.62 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.31
RfactorNum. reflection% reflection
Rfree0.2318 1993 4.23 %
Rwork0.2059 --
obs0.207 47143 99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.312→29.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7804 0 68 215 8087
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0068104
X-RAY DIFFRACTIONf_angle_d0.81111052
X-RAY DIFFRACTIONf_dihedral_angle_d16.2982878
X-RAY DIFFRACTIONf_chiral_restr0.0561148
X-RAY DIFFRACTIONf_plane_restr0.0051436
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3118-2.36950.34511270.27782883X-RAY DIFFRACTION91
2.3695-2.43360.33311420.26093198X-RAY DIFFRACTION100
2.4336-2.50520.29881420.25183212X-RAY DIFFRACTION99
2.5052-2.5860.27091400.2333181X-RAY DIFFRACTION99
2.586-2.67830.28171410.24523209X-RAY DIFFRACTION100
2.6783-2.78550.28571440.23673204X-RAY DIFFRACTION99
2.7855-2.91220.27341420.23323236X-RAY DIFFRACTION100
2.9122-3.06560.27431410.23763223X-RAY DIFFRACTION100
3.0656-3.25740.21961440.22853251X-RAY DIFFRACTION100
3.2574-3.50860.21481410.21873209X-RAY DIFFRACTION100
3.5086-3.8610.22241430.19663256X-RAY DIFFRACTION100
3.861-4.41820.19181440.16523276X-RAY DIFFRACTION100
4.4182-5.56080.17911480.17093342X-RAY DIFFRACTION100
5.5608-30.16490.22111540.18873470X-RAY DIFFRACTION100

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