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- PDB-6kxn: Crystal structure of W50A mutant of Chitiniphilus shinanonensis c... -

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Basic information

Entry
Database: PDB / ID: 6kxn
TitleCrystal structure of W50A mutant 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


endochitinase activity / chitinase / chitin catabolic process / chitin binding / carbohydrate metabolic process
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 / Glycosyl hydrolases family 18 (GH18) domain profile. / Glycoside hydrolase family 18, catalytic domain / Glycoside hydrolase superfamily
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / chitinase
Similarity search - Component
Biological speciesChitiniphilus shinanonensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 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
Revision 1.2Nov 13, 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)84,62517
Polymers82,5462
Non-polymers2,08015
Water13,709761
1
A: Family 18 chitinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,3709
Polymers41,2731
Non-polymers1,0978
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area180 Å2
ΔGint-13 kcal/mol
Surface area14750 Å2
MethodPISA
2
B: Family 18 chitinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,2568
Polymers41,2731
Non-polymers9837
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area14820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.406, 81.230, 130.264
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 / Sugars , 2 types, 4 molecules AB

#1: Protein Family 18 chitinase / CsChiL


Mass: 41272.809 Da / Num. of mol.: 2 / Mutation: W50A
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
#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, 774 molecules

#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 761 / 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: 2.22 Å3/Da / Density % sol: 44.7 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / Details: Tris-HCl, Ammonium sulfate, PEG 3350

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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: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 28, 2016 / 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: 1.5→50 Å / Num. obs: 117599 / % possible obs: 99.4 % / Redundancy: 5.5 % / Rmerge(I) obs: 0.104 / Rpim(I) all: 0.048 / Rrim(I) all: 0.115 / Χ2: 0.981 / Net I/av σ(I): 10.51 / Net I/σ(I): 10.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.5-1.5550.6382.7116230.8820.3120.7131.02499.4
1.55-1.625.20.5312.97116510.9020.2550.5921.01899.6
1.62-1.695.20.4373.14116920.9190.2090.4861.00499.7
1.69-1.785.30.3623.36116760.9360.1710.4020.98699.7
1.78-1.895.40.2883.67117080.9490.1350.3190.96699.8
1.89-2.045.50.2354.25117590.9560.1090.260.97299.7
2.04-2.245.70.1795.52117570.9750.0810.1970.96499.8
2.24-2.565.90.1377.49118570.9830.0620.1510.96599.9
2.56-3.2360.0912.25119170.9920.0410.0990.97499.7
3.23-505.70.05721.54119590.9950.0260.0630.95196.9

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Processing

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

6kxl


Resolution: 1.5→31.02 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.91 / Matrix type: sparse / SU B: 3.266 / SU ML: 0.118 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.109 / ESU R Free: 0.11
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2929 5867 5 %RANDOM
Rwork0.2533 ---
obs0.2553 111222 98.54 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 64.76 Å2 / Biso mean: 19.737 Å2 / Biso min: 11.06 Å2
Baniso -1Baniso -2Baniso -3
1--1.59 Å20 Å20 Å2
2--2.6 Å20 Å2
3----1.01 Å2
Refinement stepCycle: final / Resolution: 1.5→31.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5798 0 127 766 6691
Biso mean--28.37 28.39 -
Num. residues----735
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0136088
X-RAY DIFFRACTIONr_bond_other_d0.0020.0185396
X-RAY DIFFRACTIONr_angle_refined_deg1.3781.6568256
X-RAY DIFFRACTIONr_angle_other_deg1.3151.60712526
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.085743
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.2622.901324
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.56915952
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.8621530
X-RAY DIFFRACTIONr_chiral_restr0.0670.2755
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.026884
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021358
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.5370.3634060.3467679X-RAY DIFFRACTION92.984
1.537-1.5790.3514530.3287977X-RAY DIFFRACTION99.516
1.579-1.6250.3534420.327762X-RAY DIFFRACTION99.575
1.625-1.6750.3733640.3217592X-RAY DIFFRACTION99.624
1.675-1.7290.3733920.3157378X-RAY DIFFRACTION99.718
1.729-1.790.3653800.3227088X-RAY DIFFRACTION99.613
1.79-1.8580.3563630.3196838X-RAY DIFFRACTION99.489
1.858-1.9330.3473420.3176637X-RAY DIFFRACTION99.303
1.933-2.0190.3393290.316332X-RAY DIFFRACTION98.916
2.019-2.1180.3193290.2956031X-RAY DIFFRACTION99.235
2.118-2.2320.3193020.2835790X-RAY DIFFRACTION99.218
2.232-2.3670.3042920.2535459X-RAY DIFFRACTION98.916
2.367-2.530.2972620.2385136X-RAY DIFFRACTION98.883
2.53-2.7320.2792690.2344795X-RAY DIFFRACTION98.945
2.732-2.9920.2692290.2364423X-RAY DIFFRACTION98.79
2.992-3.3440.2832010.2244043X-RAY DIFFRACTION98.698
3.344-3.8580.241800.2043490X-RAY DIFFRACTION96.174
3.858-4.7180.2151640.1842924X-RAY DIFFRACTION95.338
4.718-6.6430.2311160.1922448X-RAY DIFFRACTION99.767
6.643-31.020.189520.2041394X-RAY DIFFRACTION95.069

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