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- PDB-7c92: Structure of Serratia marcescens chitinase B complexed with compo... -

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Basic information

Entry
Database: PDB / ID: 7c92
TitleStructure of Serratia marcescens chitinase B complexed with compound 6k
ComponentsChitinase
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-FXR / chitinase
Similarity search - Component
Biological speciesSerratia marcescens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.32 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: Yuan, P.T. / Jiang, X.
History
DepositionJun 4, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 9, 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 9, 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: Chitinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,6005
Polymers113,5192
Non-polymers1,0813
Water7,909439
1
A: Chitinase
hetero molecules

B: Chitinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,6005
Polymers113,5192
Non-polymers1,0813
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x+1/2,-y,z+1/21
Buried area3080 Å2
ΔGint-13 kcal/mol
Surface area36900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.362, 103.644, 186.792
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


Mass: 56759.254 Da / Num. of mol.: 2 / Fragment: UNP residues 2-499
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Serratia marcescens (bacteria) / Gene: chiB / Production host: Escherichia coli (E. coli) / References: UniProt: Q54276
#2: Chemical ChemComp-FXR / 6-azanyl-11-methyl-2-oxidanylidene-N-(pyridin-3-ylmethyl)-1,7,9-triazatricyclo[8.4.0.0^3,8]tetradeca-3(8),4,6,9,11,13-hexaene-5-carboxamide


Mass: 360.369 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C19H16N6O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 439 / 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: 2.45 Å3/Da / Density % sol: 49.7 %
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 S 6M / Detector: PIXEL / Date: Oct 16, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.316→48.88 Å / Num. obs: 46796 / % possible obs: 93.56 % / Redundancy: 8.6 % / Biso Wilson estimate: 33.74 Å2 / R split: 0.058 / Rpim(I) all: 0.061 / Net I/σ(I): 9.6
Reflection shellResolution: 2.32→2.36 Å / Num. unique obs: 2418 / R split: 0.234 / Rpim(I) all: 0.234

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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: 2.32→48.88 Å / SU ML: 0.2803 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.8726 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflection
Rfree0.2299 1978 4.28 %
Rwork0.1726 44250 -
obs0.175 46228 93.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 34.26 Å2
Refinement stepCycle: LAST / Resolution: 2.32→48.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7778 0 81 439 8298
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00728122
X-RAY DIFFRACTIONf_angle_d0.8511082
X-RAY DIFFRACTIONf_chiral_restr0.04851144
X-RAY DIFFRACTIONf_plane_restr0.00531436
X-RAY DIFFRACTIONf_dihedral_angle_d4.25874650
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.32-2.370.3129880.20811989X-RAY DIFFRACTION59.62
2.37-2.440.3361150.21212537X-RAY DIFFRACTION77.18
2.44-2.510.29031360.20543023X-RAY DIFFRACTION90.33
2.51-2.590.29161440.19773216X-RAY DIFFRACTION96.25
2.59-2.680.2721450.20583230X-RAY DIFFRACTION97.29
2.68-2.790.25781470.19873286X-RAY DIFFRACTION98.31
2.79-2.920.30551490.19213320X-RAY DIFFRACTION99.34
2.92-3.070.27181480.18163341X-RAY DIFFRACTION99.54
3.07-3.260.21271500.17713351X-RAY DIFFRACTION99.69
3.26-3.520.23351510.16913377X-RAY DIFFRACTION99.83
3.52-3.870.2091510.15873381X-RAY DIFFRACTION99.83
3.87-4.430.19921520.14233406X-RAY DIFFRACTION99.58
4.43-5.580.19231530.15613388X-RAY DIFFRACTION98.83
5.58-100.19181490.17453405X-RAY DIFFRACTION93.82

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