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

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Basic information

Entry
Database: PDB / ID: 6jkf
TitleCrystal structure of Serratia marcescens Chitinase B complexed with compound 2-8-s2
ComponentsChitinase
KeywordsHYDROLASE / chitinase / complex / Serratia marcescens
Function / homology
Function and homology information


chitinase / chitinase activity / 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. / Glycoside hydrolase family 18, catalytic domain ...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. / Glycoside hydrolase family 18, catalytic domain / Glycosyl hydrolases family 18 / Glycoside hydrolase superfamily
Similarity search - Domain/homology
Chem-BV0 / Chitinase B / Chitinase
Similarity search - Component
Biological speciesSerratia marcescens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.99 Å
AuthorsYang, Q. / Jiang, X.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31425021 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 28, 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

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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)111,9365
Polymers110,5992
Non-polymers1,3363
Water12,448691
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3130 Å2
ΔGint-12 kcal/mol
Surface area36950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.767, 104.997, 185.868
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


Mass: 55299.742 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-BV0 / 6-azanyl-11-methyl-2-oxidanylidene-7-[[(2R)-oxolan-2-yl]methyl]-N-(pyridin-3-ylmethyl)-1,9-diaza-7-azoniatricyclo[8.4.0.0^{3,8}]tetradeca-3(8),4,6,9,11,13-hexaene-5-carboxamide


Mass: 445.494 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C24H25N6O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 691 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.46 Å3/Da / Density % sol: 50.03 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 50 mM citrate (pH 5.6), 0.5 M Li2SO4, and 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: 1.99→29.712 Å / Num. obs: 75549 / % possible obs: 100 % / Redundancy: 13.1 % / Rsym value: 0.109 / Net I/σ(I): 25.5
Reflection shellResolution: 2→2.03 Å / Redundancy: 13.3 % / Mean I/σ(I) obs: 4.4 / Num. unique obs: 3683 / Rsym value: 0.375 / % 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: 1.99→29.712 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.85
RfactorNum. reflection% reflection
Rfree0.2014 1998 2.65 %
Rwork0.1821 --
obs0.1826 75427 99.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.99→29.712 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7809 0 99 691 8599
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0058144
X-RAY DIFFRACTIONf_angle_d0.7911110
X-RAY DIFFRACTIONf_dihedral_angle_d14.0222905
X-RAY DIFFRACTIONf_chiral_restr0.0491149
X-RAY DIFFRACTIONf_plane_restr0.0041438
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9901-2.03990.23281320.20644892X-RAY DIFFRACTION95
2.0399-2.0950.24581410.20165175X-RAY DIFFRACTION100
2.095-2.15670.24681430.19825220X-RAY DIFFRACTION100
2.1567-2.22620.25651420.19335214X-RAY DIFFRACTION100
2.2262-2.30580.23081410.18635175X-RAY DIFFRACTION100
2.3058-2.39810.19261420.18665231X-RAY DIFFRACTION100
2.3981-2.50720.21281420.18585222X-RAY DIFFRACTION100
2.5072-2.63930.21011430.19215250X-RAY DIFFRACTION100
2.6393-2.80450.23831420.19515236X-RAY DIFFRACTION100
2.8045-3.02090.21421430.195259X-RAY DIFFRACTION100
3.0209-3.32450.21191440.18585281X-RAY DIFFRACTION100
3.3245-3.80470.18941460.17325317X-RAY DIFFRACTION100
3.8047-4.79030.13721450.15355371X-RAY DIFFRACTION100
4.7903-29.7120.211520.18885586X-RAY DIFFRACTION100

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