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

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Basic information

Entry
Database: PDB / ID: 8yui
TitleX-ray Crystal structure of glycoside hydrolase family 18 chitinase from Serratia marcescens hexahistigine-tagged SmChiB with triacetyl chitotriose
ComponentsChitinase B
KeywordsHYDROLASE / glycoside hydrolase family 18 GH18 chitinase hexahistigine-tag triacetyl chitotriose
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 ...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 / Glycosyl hydrolases family 18 (GH18) domain profile. / Glycoside hydrolase family 18, catalytic domain / Glycoside hydrolase superfamily
Similarity search - Domain/homology
ACETATE ION / Chem-NGO / PHOSPHATE ION / Chitinase B
Similarity search - Component
Biological speciesSerratia marcescens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.43 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 with triacetyl chitotriose
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
B: Chitinase B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,83998
Polymers113,8252
Non-polymers9,01496
Water28,4821581
1
A: Chitinase B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,51250
Polymers56,9131
Non-polymers4,59949
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Chitinase B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,32848
Polymers56,9131
Non-polymers4,41547
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)97.380, 97.380, 197.347
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

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Protein / Sugars , 2 types, 4 molecules AB

#1: Protein Chitinase B


Mass: 56912.523 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Serratia marcescens (bacteria) / Strain: QMB1466 / Gene: chiB / Plasmid: pET-22b(+) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P11797, chitinase
#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE

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Non-polymers , 5 types, 1675 molecules

#3: Chemical...
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 66 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-NGO / 2-METHYL-4,5-DIHYDRO-(1,2-DIDEOXY-ALPHA-D-GLUCOPYRANOSO)[2,1-D]-1,3-OXAZOLE / N-ACETYLGLUCOSAMINE-OXAZOLINIUM ION INTERMEDIATE


Mass: 204.200 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H14NO5 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical...
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 22 / Source method: obtained synthetically / Formula: C2H3O2
#6: Chemical
ChemComp-PO4 / PHOSPHATE ION


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


Mass: 18.015 Da / Num. of mol.: 1581 / Source method: isolated from a natural source / Formula: H2O

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Details

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

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: Mar 11, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.43→48.69 Å / Num. obs: 344210 / % possible obs: 99.93 % / Redundancy: 13.4 % / Biso Wilson estimate: 19.39 Å2 / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.06641 / Rpim(I) all: 0.01872 / Rrim(I) all: 0.06903 / Net I/σ(I): 19.72
Reflection shellResolution: 1.43→1.481 Å / Redundancy: 13.4 % / Rmerge(I) obs: 1.723 / Mean I/σ(I) obs: 1.61 / Num. unique obs: 34167 / CC1/2: 0.757 / CC star: 0.929 / Rpim(I) all: 0.4864 / Rrim(I) all: 1.791 / % possible all: 99.93

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
PHENIX1.19.2_4158refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.43→48.69 Å / SU ML: 0.1258 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 16.8493
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1382 2008 5.8 %
Rwork0.1238 341977 -
obs0.1239 343985 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 28.95 Å2
Refinement stepCycle: LAST / Resolution: 1.43→48.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7831 0 590 1581 10002
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00619394
X-RAY DIFFRACTIONf_angle_d0.83712760
X-RAY DIFFRACTIONf_chiral_restr0.08021292
X-RAY DIFFRACTIONf_plane_restr0.00731669
X-RAY DIFFRACTIONf_dihedral_angle_d9.48971439
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.43-1.470.26931430.245424170X-RAY DIFFRACTION99.84
1.47-1.510.24841390.214924217X-RAY DIFFRACTION99.78
1.51-1.550.2151410.195524289X-RAY DIFFRACTION99.92
1.55-1.60.21051390.169624245X-RAY DIFFRACTION99.87
1.6-1.660.20531460.161224246X-RAY DIFFRACTION99.89
1.66-1.720.18211410.14124258X-RAY DIFFRACTION99.94
1.72-1.80.17741460.129124356X-RAY DIFFRACTION99.96
1.8-1.90.15171400.108624326X-RAY DIFFRACTION99.97
1.9-2.020.13811460.113324364X-RAY DIFFRACTION99.98
2.02-2.170.12611420.105824426X-RAY DIFFRACTION99.99
2.17-2.390.14341450.121224500X-RAY DIFFRACTION100
2.39-2.740.12791440.12124540X-RAY DIFFRACTION99.99
2.74-3.450.1191460.119424732X-RAY DIFFRACTION100
3.45-48.690.11791500.111825308X-RAY DIFFRACTION99.9

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