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

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Basic information

Entry
Database: PDB / ID: 8yuh
TitleX-ray Crystal structure of glycoside hydrolase family 18 chitinase from Serratia marcescens hexahistigine-tagged SmChiB with allosamidin
ComponentsChitinase B
KeywordsHYDROLASE / glycoside hydrolase family 18 GH18 chitinase hexahistigine-tag allosamidin
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
Allosamidin / ACETATE ION / ALLOSAMIZOLINE / PHOSPHATE ION / Chitinase B
Similarity search - Component
Biological speciesSerratia marcescens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.73 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 allosamidin
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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)124,580116
Polymers113,8252
Non-polymers10,755114
Water28,3201572
1
A: Chitinase B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,47061
Polymers56,9131
Non-polymers5,55860
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Chitinase B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,11055
Polymers56,9131
Non-polymers5,19854
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)97.850, 97.850, 196.678
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number78
Space group name H-MP43
Space group name HallP4cw
Symmetry operation#1: x,y,z
#2: -y,x,z+3/4
#3: y,-x,z+1/4
#4: -x,-y,z+1/2

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Components

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Protein / Sugars , 2 types, 6 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-allopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-allopyranose


Type: oligosaccharide, Oligosaccharide / Class: Inhibitor / Mass: 424.401 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
References: Allosamidin
DescriptorTypeProgram
DAllpNAcb1-4DAllpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2222h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-AllpNAc]{[(4+1)][b-D-AllpNAc]{}}LINUCSPDB-CARE

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Non-polymers , 5 types, 1682 molecules

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


Mass: 92.094 Da / Num. of mol.: 52 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: PO4
#5: Chemical...
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 48 / Source method: obtained synthetically / Formula: C2H3O2
#6: Chemical
ChemComp-AMI / ALLOSAMIZOLINE


Type: Oligosaccharide / Class: Inhibitor / Mass: 216.234 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C9H16N2O4 / Feature type: SUBJECT OF INVESTIGATION / References: Allosamidin
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1572 / 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

CrystalDensity Matthews: 4.14 Å3/Da / Density % sol: 70.26 %
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: 1.73→47.59 Å / Num. obs: 191652 / % possible obs: 99.96 % / Redundancy: 13.8 % / Biso Wilson estimate: 22.14 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.1239 / Rpim(I) all: 0.03456 / Rrim(I) all: 0.1287 / Net I/σ(I): 15.66
Reflection shellResolution: 1.73→1.76 Å / Redundancy: 13.1 % / Rmerge(I) obs: 1.688 / Mean I/σ(I) obs: 1.68 / Num. unique obs: 19068 / CC1/2: 0.7 / CC star: 0.908 / Rpim(I) all: 0.4841 / Rrim(I) all: 1.756 / % possible all: 99.95

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.73→47.59 Å / SU ML: 0.1806 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.0672
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1699 2010 1.05 %
Rwork0.1536 189582 -
obs0.1538 191592 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 27.1 Å2
Refinement stepCycle: LAST / Resolution: 1.73→47.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7836 0 706 1572 10114
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00779547
X-RAY DIFFRACTIONf_angle_d1.021112957
X-RAY DIFFRACTIONf_chiral_restr0.05851336
X-RAY DIFFRACTIONf_plane_restr0.00711697
X-RAY DIFFRACTIONf_dihedral_angle_d9.0531379
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.73-1.770.29811410.280913514X-RAY DIFFRACTION99.96
1.77-1.820.29461470.252413496X-RAY DIFFRACTION99.95
1.82-1.870.23691480.220613549X-RAY DIFFRACTION99.96
1.87-1.940.26341420.210913453X-RAY DIFFRACTION99.96
1.94-20.17861410.185113582X-RAY DIFFRACTION99.99
2-2.080.20091460.172113507X-RAY DIFFRACTION99.98
2.08-2.180.17421430.169913549X-RAY DIFFRACTION99.99
2.18-2.290.16741380.159213502X-RAY DIFFRACTION99.96
2.29-2.440.15781420.154813534X-RAY DIFFRACTION99.99
2.44-2.630.17211420.151813527X-RAY DIFFRACTION100
2.63-2.890.17571470.1613591X-RAY DIFFRACTION100
2.89-3.310.14331430.140113533X-RAY DIFFRACTION99.99
3.31-4.170.13521470.122613583X-RAY DIFFRACTION100
4.17-47.590.15621430.127413662X-RAY DIFFRACTION99.83

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