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- PDB-6lwu: Complex of Gynuella sunshinyii GH46 chitosanase GsCsn46A E19A wit... -

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Basic information

Entry
Database: PDB / ID: 6lwu
TitleComplex of Gynuella sunshinyii GH46 chitosanase GsCsn46A E19A with chitopentaose
Componentschitosanase
KeywordsHYDROLASE / chitosanase / glucoside hydrolase / GH46
Function / homologyGlycoside hydrolase, family 46, N-terminal / Glycosyl hydrolase family 46 / chitosanase activity / Glycoside hydrolase, family 46 / Lysozyme-like domain superfamily / carbohydrate metabolic process / extracellular region / 2-amino-2-deoxy-beta-D-glucopyranose / Chitosanase
Function and homology information
Biological speciesGynuella sunshinyii YC6258 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.419 Å
AuthorsQin, Z. / Wang, Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31701537 China
CitationJournal: To Be Published
Title: Complex of Gynuella sunshinyii GH46 chitosanase GsCsn46A E19A with chitopentaose
Authors: Qin, Z. / Wang, Y.
History
DepositionFeb 9, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 10, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 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: chitosanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,9174
Polymers27,0581
Non-polymers8603
Water93752
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1680 Å2
ΔGint15 kcal/mol
Surface area10950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.644, 83.644, 118.274
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3

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Components

#1: Protein chitosanase


Mass: 27057.549 Da / Num. of mol.: 1 / Mutation: E42A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gynuella sunshinyii YC6258 (bacteria) / Gene: YC6258_05941
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A0A0C5VFC0
#2: Polysaccharide 2-amino-2-deoxy-beta-D-glucopyranose-(1-4)-2-amino-2-deoxy-beta-D-glucopyranose-(1-4)-2-amino-2- ...2-amino-2-deoxy-beta-D-glucopyranose-(1-4)-2-amino-2-deoxy-beta-D-glucopyranose-(1-4)-2-amino-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 501.483 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNb1-4DGlcpNb1-4DGlcpNb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,3,2/[a2122h-1b_1-5_2*N]/1-1-1/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpN]{[(4+1)][b-D-GlcpN]{[(4+1)][b-D-GlcpN]{}}}LINUCSPDB-CARE
#3: Sugar ChemComp-GCS / 2-amino-2-deoxy-beta-D-glucopyranose / beta-D-glucosamine / 2-amino-2-deoxy-beta-D-glucose / 2-amino-2-deoxy-D-glucose / 2-amino-2-deoxy-glucose / D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 179.171 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C6H13NO5 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGlcpNbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 52 / Source method: isolated from a natural source / Formula: H2O
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: 2.95 Å3/Da / Density % sol: 58.31 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1M HEPES, 10%PEG 8000, 8% (v/v) glycol,2% (w/v) chitopentaose

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-BM / Wavelength: 0.9792 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Dec 8, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.419→50 Å / Num. obs: 11676 / % possible obs: 99.2 % / Redundancy: 9.7 % / Rmerge(I) obs: 0.043 / Rpim(I) all: 0.015 / Rrim(I) all: 0.046 / Χ2: 0.811 / Net I/σ(I): 12.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.42-2.469.50.0945880.9980.0320.0990.62799.8
2.46-2.518.80.0945880.9980.0330.10.67699.5
2.51-2.559.70.0895830.9980.030.0940.6999.1
2.55-2.6110.50.0875800.9980.0290.0920.65100
2.61-2.66100.0835940.9990.0280.0880.703100
2.66-2.73100.0835880.9990.0280.0870.893100
2.73-2.7910.40.0696080.9990.0230.0720.67499.8
2.79-2.8710.20.0625580.9990.0210.0650.667100
2.87-2.9510.10.066000.9980.020.0640.692100
2.95-3.05100.0565780.9990.0190.0590.7299.8
3.05-3.169.90.055800.9990.0170.0520.74699.8
3.16-3.289.50.0476010.9990.0160.050.78999.2
3.28-3.438.80.0445780.9980.0160.0470.87497.6
3.43-3.618.40.0465780.9990.0160.0491.15898
3.61-3.8490.0415570.9990.0140.0441.23696.9
3.84-4.149.50.045940.9990.0140.0421.37599
4.14-4.559.80.0325720.9990.0110.0340.79197.4
4.55-5.21100.0325900.9990.0110.0340.74699.8
5.21-6.569.90.0345750.9990.0110.0350.70399.3
6.56-5010.10.0345860.9990.0110.0360.94398.5

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
HKL-2000data scaling
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4OLT

4olt


Resolution: 2.419→45.81 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 2.05 / Phase error: 30.18
RfactorNum. reflection% reflection
Rfree0.2556 1179 10.1 %
Rwork0.1994 --
obs0.205 11676 99.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 79.43 Å2 / Biso mean: 35.8523 Å2 / Biso min: 17.33 Å2
Refinement stepCycle: final / Resolution: 2.419→45.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1883 0 56 52 1991
Biso mean--42.59 33.89 -
Num. residues----242
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.419-2.52910.31721490.2274129899
2.5291-2.66240.281490.22811324100
2.6624-2.82920.30571460.22041317100
2.8292-3.04760.32771500.24621324100
3.0476-3.35420.30461480.2439132599
3.3542-3.83940.27891440.2074128597
3.8394-4.83630.2081450.1629131499
4.8363-9.90.17581480.1557131099

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