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- PDB-6kst: Crystal structure of the catalytic domain of chitinase ChiL from ... -

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Basic information

Entry
Database: PDB / ID: 6kst
TitleCrystal structure of the catalytic domain of chitinase ChiL from Chitiniphilus shinanonensis (CsChiL)
ComponentsFamily 18 chitinase
KeywordsHYDROLASE / Chitin / Chitinase / Chitinolytic enzyme / Family 18 glycoside hydrolase (GH18) / N-acetylglucosamine (GlcNAc) / Hydrolysis / Transglycosylation
Function / homology
Function and homology information


chitin binding / polysaccharide catabolic process / hydrolase activity, hydrolyzing O-glycosyl compounds
Similarity search - Function
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
2-METHOXYETHANOL / Family 18 chitinase
Similarity search - Component
Biological speciesChitiniphilus shinanonensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.25 Å
AuthorsUeda, M. / Shimosaka, M. / Arai, R.
Funding support Japan, 7items
OrganizationGrant numberCountry
Japan Society for the Promotion of ScienceJP24780097 Japan
Japan Society for the Promotion of ScienceJP24580107
Japan Society for the Promotion of ScienceJP24113707
Japan Society for the Promotion of ScienceJP16K05841
Japan Society for the Promotion of ScienceJP16H00761
Japan Society for the Promotion of ScienceJP17KK0104
Japan Society for the Promotion of ScienceJP19H02522
Citation
Journal: To be published
Title: Crystal structure of a chitinase (CsChiL) from Chitiniphilus shinanonensis
Authors: Ueda, M. / Sonoda, N. / Shimosaka, M. / Arai, R.
#1: Journal: Acta Crystallogr F Struct Biol Commun / Year: 2015
Title: Expression, purification, crystallization and X-ray diffraction analysis of ChiL, a chitinase from Chitiniphilus shinanonensis.
Authors: Ueda, M. / Shimosaka, M. / Arai, R.
History
DepositionAug 26, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 26, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 22, 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: Family 18 chitinase
B: Family 18 chitinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,54223
Polymers82,7762
Non-polymers1,76621
Water27,2391512
1
A: Family 18 chitinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,39912
Polymers41,3881
Non-polymers1,01111
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area210 Å2
ΔGint-15 kcal/mol
Surface area14700 Å2
MethodPISA
2
B: Family 18 chitinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,14411
Polymers41,3881
Non-polymers75610
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area14860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.189, 81.547, 130.012
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Family 18 chitinase


Mass: 41387.938 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chitiniphilus shinanonensis (bacteria) / Strain: DSM 23277 / Gene: chiL / Plasmid: pCold-ChiL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Star (DE3) / References: UniProt: F8WSX2

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Non-polymers , 6 types, 1533 molecules

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


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical
ChemComp-MXE / 2-METHOXYETHANOL


Mass: 76.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O2
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1512 / Source method: isolated from a natural source / Formula: H2O

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Details

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

CrystalDensity Matthews: 2.22 Å3/Da / Density % sol: 44.48 % / Description: Plate-like crystal
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.1 M Tris-HCl, 0.2 M ammonium sulfate, 25% PEG 3350

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Data collection

DiffractionMean temperature: 95 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Dec 13, 2014 / Details: Focusing Mirror
RadiationMonochromator: Numerical link type Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.25→50 Å / Num. obs: 197591 / % possible obs: 97.3 % / Redundancy: 5.9 % / Biso Wilson estimate: 11.4 Å2 / Rpim(I) all: 0.027 / Rrim(I) all: 0.066 / Rsym value: 0.061 / Χ2: 1.009 / Net I/σ(I): 25.3
Reflection shellResolution: 1.25→1.29 Å / Redundancy: 2.6 % / Mean I/σ(I) obs: 3.6 / Num. unique obs: 16344 / CC1/2: 0.903 / Rpim(I) all: 0.208 / Rrim(I) all: 0.348 / Rsym value: 0.276 / Χ2: 1.038 / % possible all: 81.3

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 54.37 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å27.67 Å
Translation2.5 Å27.67 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0253refinement
HKL-2000data scaling
PHASER2.1.4phasing
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ITX

1itx


Resolution: 1.25→27.69 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.968 / Matrix type: sparse / SU B: 1.277 / SU ML: 0.025 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.043 / ESU R Free: 0.042
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1606 9893 5 %RANDOM
Rwork0.1324 ---
obs0.1338 186349 96.66 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 70.88 Å2 / Biso mean: 13.675 Å2 / Biso min: 7.23 Å2
Baniso -1Baniso -2Baniso -3
1--0.91 Å20 Å20 Å2
2--1.53 Å20 Å2
3----0.62 Å2
Refinement stepCycle: final / Resolution: 1.25→27.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5834 0 100 1520 7454
Biso mean--22.92 29.53 -
Num. residues----739
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0136278
X-RAY DIFFRACTIONr_bond_other_d0.0150.0175577
X-RAY DIFFRACTIONr_angle_refined_deg1.3451.6438532
X-RAY DIFFRACTIONr_angle_other_deg1.7151.59112967
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5635791
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.85322.92339
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.11151004
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.981532
X-RAY DIFFRACTIONr_chiral_restr0.0690.2760
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.027223
X-RAY DIFFRACTIONr_gen_planes_other0.0080.021417
X-RAY DIFFRACTIONr_rigid_bond_restr1.584311855
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.25-1.2820.2525850.2211047X-RAY DIFFRACTION78.162
1.282-1.3170.2186300.17812911X-RAY DIFFRACTION93.27
1.317-1.3560.187320.14813217X-RAY DIFFRACTION98.873
1.356-1.3970.1926850.14612950X-RAY DIFFRACTION99.584
1.397-1.4430.176390.1312619X-RAY DIFFRACTION99.49
1.443-1.4940.176460.12812076X-RAY DIFFRACTION99.019
1.494-1.550.1526580.12411599X-RAY DIFFRACTION98.513
1.55-1.6130.1486030.11211234X-RAY DIFFRACTION98.839
1.613-1.6850.1585820.11110788X-RAY DIFFRACTION98.956
1.685-1.7670.1525300.11110346X-RAY DIFFRACTION98.738
1.767-1.8630.1495080.1119829X-RAY DIFFRACTION98.495
1.863-1.9760.1324890.1159330X-RAY DIFFRACTION99.072
1.976-2.1120.1454750.1258836X-RAY DIFFRACTION99.498
2.112-2.2810.144440.1158248X-RAY DIFFRACTION99.622
2.281-2.4980.143700.1147644X-RAY DIFFRACTION99.677
2.498-2.7930.1383760.1226919X-RAY DIFFRACTION99.74
2.793-3.2240.1513570.1326085X-RAY DIFFRACTION99.475
3.224-3.9470.1692750.1364913X-RAY DIFFRACTION93.883
3.947-5.5720.2032060.1753707X-RAY DIFFRACTION90.141
5.572-27.690.2441030.2522052X-RAY DIFFRACTION85.077

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