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- PDB-6kxl: Crystal structure of the catalytic domain of Chitiniphilus shinan... -

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Basic information

Entry
Database: PDB / ID: 6kxl
TitleCrystal structure of the catalytic domain of Chitiniphilus shinanonensis chitinase ChiL (CsChiL) complexed with N,N'-diacetylchitobiose
ComponentsFamily 18 chitinase
KeywordsHYDROLASE / Chitin / Chitinase / Chitinolytic enzyme / Family 18 glycoside hydrolase (GH18) / N-acetylglucosamine (GlcNAc) / Hydrolysis / Transglycosylation / Enzyme-product complex
Function / homology
Function and homology information


chitinase activity / chitin catabolic process / chitin binding / polysaccharide catabolic process / extracellular region
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. / Glycoside hydrolase family 18, catalytic domain / Glycosyl hydrolases family 18 / Glycoside hydrolase superfamily
Similarity search - Domain/homology
ACETATE ION / MALONATE ION / 2-METHOXYETHANOL / TRIETHYLENE GLYCOL / Family 18 chitinase
Similarity search - Component
Biological speciesChitiniphilus shinanonensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.35 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
Japan Society for the Promotion of ScienceJP24113707 Japan
Japan Society for the Promotion of ScienceJP16K05841 Japan
Japan Society for the Promotion of ScienceJP16H00761 Japan
Japan Society for the Promotion of ScienceJP17KK0104 Japan
Japan Society for the Promotion of ScienceJP19H02522 Japan
Citation
Journal: To be published
Title: Crystal structure of CsChiL, a chitinase 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
DepositionSep 12, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 16, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Family 18 chitinase
B: Family 18 chitinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,96524
Polymers82,7762
Non-polymers3,18922
Water21,7981210
1
A: Family 18 chitinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,81112
Polymers41,3881
Non-polymers1,42311
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area150 Å2
ΔGint-0 kcal/mol
Surface area14870 Å2
MethodPISA
2
B: Family 18 chitinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,15412
Polymers41,3881
Non-polymers1,76611
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area160 Å2
ΔGint-1 kcal/mol
Surface area14760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.982, 82.502, 131.818
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 / Chitinase CsChiL


Mass: 41387.938 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chitiniphilus shinanonensis (bacteria) / Strain: SAY3 / Gene: chiL / Plasmid: pCold-ChiL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Star (DE3) / References: UniProt: F8WSX2

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Sugars , 2 types, 4 molecules

#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: obtained synthetically
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
#8: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 7 types, 1228 molecules

#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-MXE / 2-METHOXYETHANOL


Mass: 76.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O2
#5: Chemical
ChemComp-MLI / MALONATE ION


Mass: 102.046 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H2O4
#6: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#7: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Formula: C2H6O2
#9: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1210 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.27 Å3/Da / Density % sol: 45.71 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 0.2 M sodium malonate, 29% w/v 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: 1.35→50 Å / Num. obs: 157981 / % possible obs: 95.8 % / Redundancy: 6.7 % / Biso Wilson estimate: 12 Å2 / Rmerge(I) obs: 0.076 / Rpim(I) all: 0.031 / Rrim(I) all: 0.083 / Χ2: 1.015 / Net I/av σ(I): 22.9 / Net I/σ(I): 11.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.35-1.45.70.4424134380.9280.1970.4860.99782.5
1.4-1.456.70.3675.7157230.9620.1510.3971.02296.3
1.45-1.526.80.2797.5157720.9750.1140.3011.02296.6
1.52-1.66.80.219.6158400.9850.0850.2271.01596.6
1.6-1.76.80.16211.8158410.990.0660.1761.00796.8
1.7-1.836.80.12714.5158920.9930.0520.1371.01696.7
1.83-2.026.80.09518.5160640.9950.0380.1021.02497.5
2.02-2.316.90.07423.2163720.9960.030.081.01499.1
2.31-2.9170.06627.1165750.9970.0260.0711.01399.7
2.91-506.50.05429.8164640.9970.0230.0591.01496

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation3 Å31.19 Å
Translation3 Å31.19 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0253refinement
HKL-2000data scaling
MOLREP10.2.35phasing
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6KST

6kst


Resolution: 1.35→31.21 Å / Cor.coef. Fo:Fc: 0.982 / Cor.coef. Fo:Fc free: 0.975 / Matrix type: sparse / SU B: 1.606 / SU ML: 0.029 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.049 / ESU R Free: 0.046
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1477 7893 5 %RANDOM
Rwork0.1181 ---
obs0.1196 149276 95.21 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 64.85 Å2 / Biso mean: 15.029 Å2 / Biso min: 8.2 Å2
Baniso -1Baniso -2Baniso -3
1--0.76 Å20 Å20 Å2
2--1.25 Å20 Å2
3----0.49 Å2
Refinement stepCycle: final / Resolution: 1.35→31.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5816 0 209 1212 7237
Biso mean--26.44 30.83 -
Num. residues----735
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0136302
X-RAY DIFFRACTIONr_bond_other_d0.0180.0185634
X-RAY DIFFRACTIONr_angle_refined_deg1.3921.6698528
X-RAY DIFFRACTIONr_angle_other_deg1.6611.61513105
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5385772
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.68722.738336
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.0615989
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.1351533
X-RAY DIFFRACTIONr_chiral_restr0.0690.2781
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.027144
X-RAY DIFFRACTIONr_gen_planes_other0.0070.021409
X-RAY DIFFRACTIONr_rigid_bond_restr3.248311934
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.35-1.3850.1924910.168890X-RAY DIFFRACTION77.677
1.385-1.4230.1875660.14510501X-RAY DIFFRACTION93.86
1.423-1.4640.1785730.13410455X-RAY DIFFRACTION96.289
1.464-1.5090.1645750.1210145X-RAY DIFFRACTION96.429
1.509-1.5590.1574960.1179955X-RAY DIFFRACTION96.509
1.559-1.6140.1675240.1089535X-RAY DIFFRACTION96.351
1.614-1.6740.1625000.1049244X-RAY DIFFRACTION96.294
1.674-1.7430.1464490.1068871X-RAY DIFFRACTION96.132
1.743-1.820.1584080.1098579X-RAY DIFFRACTION95.861
1.82-1.9090.1454130.1078150X-RAY DIFFRACTION95.74
1.909-2.0120.1384080.1027854X-RAY DIFFRACTION97.006
2.012-2.1340.1334040.1017545X-RAY DIFFRACTION98.586
2.134-2.2810.1363990.0957120X-RAY DIFFRACTION99.052
2.281-2.4630.1233590.1016673X-RAY DIFFRACTION98.903
2.463-2.6980.1443150.1146174X-RAY DIFFRACTION99.038
2.698-3.0150.1513000.1255573X-RAY DIFFRACTION98.789
3.015-3.4790.1452670.1294995X-RAY DIFFRACTION99.377
3.479-4.2560.1392010.124127X-RAY DIFFRACTION96.221
4.256-5.9970.1411760.1413184X-RAY DIFFRACTION94.728
5.997-31.210.188690.2111707X-RAY DIFFRACTION85.426

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