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- PDB-7cb1: Structure of Serratia marcescens chitinase B complexed with compo... -

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Basic information

Entry
Database: PDB / ID: 7cb1
TitleStructure of Serratia marcescens chitinase B complexed with compound 6q
ComponentsChitinase B
KeywordsHYDROLASE / chitinase / Serratia marcescens
Function / homology
Function and homology information


chitinase 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-FO0 / Chitinase B
Similarity search - Component
Biological speciesSerratia marcescens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.98 Å
AuthorsJiang, X. / Yuan, P.T.
CitationJournal: To Be Published
Title: Discovery of novel Chitinase Inhibitors with a scaffold of dipyridopyrimidine-3-carboxamide via Structure-based Rational Design
Authors: Jiang, X. / Yuan, P.T.
History
DepositionJun 10, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 16, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 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 1.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Chitinase B
B: Chitinase B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,8185
Polymers113,6952
Non-polymers1,1233
Water10,683593
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2970 Å2
ΔGint-11 kcal/mol
Surface area37240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.846, 104.077, 186.286
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 Chitinase B


Mass: 56847.316 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Serratia marcescens (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: R9WYJ0, chitinase
#2: Chemical ChemComp-FO0 / 6-azanyl-11-methyl-2-oxidanylidene-N-[(1S)-1-pyridin-3-ylethyl]-1,7,9-triazatricyclo[8.4.0.0^{3,8}]tetradeca-3,5,7,9,11,13-hexaene-5-carboxamide


Mass: 374.396 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C20H18N6O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 593 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.38 Å3/Da / Density % sol: 48.42 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop
Details: 50 mM citrate (pH 5.6), 0.5 M Li2SO4 and 0.25M (NH4)2SO4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NFPSS / Beamline: BL19U1 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 17, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.97→50.12 Å / Num. obs: 67805 / % possible obs: 88 % / Redundancy: 9.8 % / Biso Wilson estimate: 23.81 Å2 / Rpim(I) all: 0.044 / Net I/σ(I): 13.98
Reflection shellResolution: 1.97→2 Å / Num. unique obs: 3271 / CC1/2: 0.884

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4g2z

4g2z


Resolution: 1.98→50.12 Å / SU ML: 0.2159 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.8443 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflection
Rfree0.2376 2000 2.95 %
Rwork0.1862 65728 -
obs0.1877 67728 87.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 26.92 Å2
Refinement stepCycle: LAST / Resolution: 1.98→50.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7792 0 84 593 8469
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00718109
X-RAY DIFFRACTIONf_angle_d0.81111065
X-RAY DIFFRACTIONf_chiral_restr0.05031151
X-RAY DIFFRACTIONf_plane_restr0.00541435
X-RAY DIFFRACTIONf_dihedral_angle_d3.09174649
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.98-2.030.2428690.2012268X-RAY DIFFRACTION43.36
2.03-2.080.3033920.19933048X-RAY DIFFRACTION57.77
2.08-2.140.28361130.19413710X-RAY DIFFRACTION70.1
2.14-2.210.23841270.20454166X-RAY DIFFRACTION79.29
2.21-2.290.27141400.20264617X-RAY DIFFRACTION88.04
2.29-2.380.24911560.19875118X-RAY DIFFRACTION96.79
2.38-2.490.27071600.19535273X-RAY DIFFRACTION99.61
2.49-2.620.21421610.19995313X-RAY DIFFRACTION99.62
2.62-2.790.27141620.18935296X-RAY DIFFRACTION99.74
2.79-30.22491610.1895314X-RAY DIFFRACTION99.82
3-3.30.23351630.18555356X-RAY DIFFRACTION99.77
3.3-3.780.24731610.17695330X-RAY DIFFRACTION99.38
3.78-4.760.21381650.16135406X-RAY DIFFRACTION99.25
4.76-50.120.22091700.19415513X-RAY DIFFRACTION97.28

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