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- PDB-8yug: X-ray Crystal structure of glycoside hydrolase family 18 chitinas... -

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Basic information

Entry
Database: PDB / ID: 8yug
TitleX-ray Crystal structure of glycoside hydrolase family 18 chitinase from Serratia marcescens hexahistigine-tagged SmChiB apo enzyme
ComponentsChitinase B
KeywordsHYDROLASE / glycoside hydrolase family 18 GH18 chitinase apo enzyme hexahistigine-tag
Function / homology
Function and homology information


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
ACETATE ION / PHOSPHATE ION / Chitinase B
Similarity search - Component
Biological speciesSerratia marcescens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.71 Å
AuthorsEbi, S. / Sunagawa, N. / Yamaguchi, S. / Igarashi, K.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: X-ray Crystal structure of glycoside hydrolase family 18 chitinase from Serratia marcescens hexahistigine-tagged SmChiB apo enzyme
Authors: Ebi, S. / Igarashi, K.
History
DepositionMar 27, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 2, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Chitinase B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,46056
Polymers56,9131
Non-polymers4,54855
Water14,142785
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)97.580, 97.580, 196.966
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Space group name HallP4nw2abw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+3/4
#3: y+1/2,-x+1/2,z+1/4
#4: x+1/2,-y+1/2,-z+1/4
#5: -x+1/2,y+1/2,-z+3/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2
Components on special symmetry positions
IDModelComponents
11A-738-

HOH

21A-919-

HOH

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Components

#1: Protein Chitinase B


Mass: 56912.523 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Serratia marcescens (bacteria) / Strain: QMB1466 / Gene: chiB / Plasmid: pET22b(+) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P11797, chitinase
#2: Chemical...
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 35 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 785 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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

Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.5 / Details: di-ammonium phosphate, sodium acetate

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Data collection

DiffractionMean temperature: 95 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 3, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.71→48.79 Å / Num. obs: 103180 / % possible obs: 99.95 % / Redundancy: 26.3 % / Biso Wilson estimate: 20.32 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.1377 / Rpim(I) all: 0.0272 / Rrim(I) all: 0.1403 / Net I/σ(I): 18.83
Reflection shellResolution: 1.71→1.771 Å / Redundancy: 25.9 % / Rmerge(I) obs: 1.408 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 10171 / CC1/2: 0.893 / CC star: 0.971 / Rpim(I) all: 0.2803 / Rrim(I) all: 1.436 / % possible all: 99.93

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.71→48.79 Å / SU ML: 0.1642 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 16.9466
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1726 2000 1.94 %
Rwork0.1518 101133 -
obs0.1522 103133 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 25.24 Å2
Refinement stepCycle: LAST / Resolution: 1.71→48.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3908 0 294 785 4987
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00684652
X-RAY DIFFRACTIONf_angle_d0.83376300
X-RAY DIFFRACTIONf_chiral_restr0.0543623
X-RAY DIFFRACTIONf_plane_restr0.0061828
X-RAY DIFFRACTIONf_dihedral_angle_d10.1356704
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.71-1.750.29441400.25857080X-RAY DIFFRACTION99.93
1.75-1.80.23191410.22827129X-RAY DIFFRACTION99.93
1.8-1.850.23021410.19667131X-RAY DIFFRACTION99.9
1.85-1.910.18541420.18187148X-RAY DIFFRACTION99.9
1.91-1.980.19961410.17247125X-RAY DIFFRACTION99.89
1.98-2.060.20261410.1667135X-RAY DIFFRACTION99.96
2.06-2.150.20861410.16777172X-RAY DIFFRACTION99.99
2.15-2.270.18261430.15227193X-RAY DIFFRACTION99.96
2.27-2.410.16841420.15167180X-RAY DIFFRACTION99.99
2.41-2.60.1861430.15247225X-RAY DIFFRACTION100
2.6-2.860.15691440.15387264X-RAY DIFFRACTION100
2.86-3.270.16541430.1427282X-RAY DIFFRACTION99.99
3.27-4.120.14161450.12347366X-RAY DIFFRACTION100
4.12-48.790.15451530.1397703X-RAY DIFFRACTION99.91

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