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- PDB-6kxm: Crystal structure of D157N mutant of Chitiniphilus shinanonensis ... -

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Basic information

Entry
Database: PDB / ID: 6kxm
TitleCrystal structure of D157N 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


chitinase / chitin catabolic process / chitin binding / hydrolase activity, hydrolyzing O-glycosyl compounds / 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 (GH18) domain profile. / Glycosyl hydrolases family 18 / Glycoside hydrolase family 18, catalytic domain / Glycoside hydrolase superfamily
Similarity search - Domain/homology
Biological speciesChitiniphilus shinanonensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.95 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)83,6234
Polymers82,7742
Non-polymers8492
Water6,648369
1
A: Family 18 chitinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,8112
Polymers41,3871
Non-polymers4241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1060 Å2
ΔGint9 kcal/mol
Surface area14170 Å2
MethodPISA
2
B: Family 18 chitinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,8112
Polymers41,3871
Non-polymers4241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1040 Å2
ΔGint10 kcal/mol
Surface area14360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.266, 81.351, 131.113
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Family 18 chitinase / CsChiL


Mass: 41386.953 Da / Num. of mol.: 2 / Mutation: D157N
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
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 369 / Source method: isolated from a natural source / Formula: H2O
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: 2.23 Å3/Da / Density % sol: 44.88 % / Description: Plate-like crystal
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 0.1 M Bis-Tris, 0.2 M NaCl, 25% w/v PEG 3350

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Data collection

DiffractionMean temperature: 97 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Dec 19, 2015 / 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: 1.95→50 Å / Num. obs: 54922 / % possible obs: 97.8 % / Redundancy: 5.7 % / Rmerge(I) obs: 0.102 / Rpim(I) all: 0.046 / Rrim(I) all: 0.112 / Χ2: 1.004 / Net I/av σ(I): 13.88 / Net I/σ(I): 8.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.95-2.025.70.6822.9254580.930.3120.7521.00399
2.02-2.15.60.4463.9854880.960.2040.491198.9
2.1-2.25.70.3455.4755000.9740.1560.381.00798.6
2.2-2.315.60.3015.1154320.9790.1370.3321.00198.2
2.31-2.465.70.2726.3354360.9840.1230.31.00397.4
2.46-2.655.60.227.0453700.9880.10.2431.00596.3
2.65-2.915.50.1746.7953140.9910.080.1921.00194.7
2.91-3.335.50.10311.5754440.9940.0480.1151.00296.9
3.33-4.260.06621.8356450.9970.0290.0721.00299.3
4.2-5060.05826.0758350.9970.0260.0631.01398.2

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Phasing

PhasingMethod: molecular replacement

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Processing

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

6kst


Resolution: 1.95→34.59 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.908 / Matrix type: sparse / SU B: 8.247 / SU ML: 0.217 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.249 / ESU R Free: 0.211
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.298 2734 5.2 %RANDOM
Rwork0.2485 ---
obs0.251 50006 96.29 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 76.48 Å2 / Biso mean: 31.626 Å2 / Biso min: 7.09 Å2
Baniso -1Baniso -2Baniso -3
1--2.18 Å20 Å20 Å2
2--5.16 Å20 Å2
3----2.98 Å2
Refinement stepCycle: final / Resolution: 1.95→34.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5796 0 58 372 6226
Biso mean--37.62 35.43 -
Num. residues----732
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0136016
X-RAY DIFFRACTIONr_bond_other_d0.0020.0175343
X-RAY DIFFRACTIONr_angle_refined_deg1.4941.6578157
X-RAY DIFFRACTIONr_angle_other_deg1.2781.60112395
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6115732
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.77422.883326
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.99415947
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.6941530
X-RAY DIFFRACTIONr_chiral_restr0.0680.2747
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.026847
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021367
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-2.0010.3781660.3723757X-RAY DIFFRACTION98.717
2.001-2.0550.382180.3513637X-RAY DIFFRACTION98.317
2.055-2.1150.3792170.3783509X-RAY DIFFRACTION98.259
2.115-2.180.3821880.333441X-RAY DIFFRACTION98.775
2.18-2.2510.3521820.323293X-RAY DIFFRACTION97.64
2.251-2.330.3581760.3163155X-RAY DIFFRACTION96.188
2.33-2.4180.3261720.2733038X-RAY DIFFRACTION96.137
2.418-2.5160.3891630.2812879X-RAY DIFFRACTION94.885
2.516-2.6280.4261240.3072723X-RAY DIFFRACTION92.315
2.628-2.7560.3621170.3092578X-RAY DIFFRACTION90.074
2.756-2.9040.3441260.2742410X-RAY DIFFRACTION89.993
2.904-3.080.3211330.2572283X-RAY DIFFRACTION90.793
3.08-3.2910.2931290.2312329X-RAY DIFFRACTION97.039
3.291-3.5540.31390.2292197X-RAY DIFFRACTION99.447
3.554-3.8910.2641120.2012055X-RAY DIFFRACTION99.086
3.891-4.3470.2331010.1821870X-RAY DIFFRACTION98.946
4.347-5.0130.2141030.1741648X-RAY DIFFRACTION99.376
5.013-6.1250.195870.1761423X-RAY DIFFRACTION99.67
6.125-8.5970.244490.1881153X-RAY DIFFRACTION99.586
8.597-34.590.185320.197618X-RAY DIFFRACTION89.163

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