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- PDB-7c6d: Crystal structure of E19A mutant chitosanase from Bacillus subtil... -

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Basic information

Entry
Database: PDB / ID: 7c6d
TitleCrystal structure of E19A mutant chitosanase from Bacillus subtilis MY002 complexed with 6 GlcN.
ComponentsChitosanase
KeywordsHYDROLASE / chitosanase
Function / homology
Function and homology information


chitosanase / chitosanase activity / carbohydrate metabolic process / extracellular region
Similarity search - Function
Chitosanases families 46 and 80 active sites signature. / Glycoside hydrolase, family 46, N-terminal / Glycosyl hydrolase family 46 / Glycoside hydrolase, family 46 / Lysozyme-like domain superfamily
Similarity search - Domain/homology
Biological speciesBacillus subtilis subsp. subtilis str. 168 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.451 Å
AuthorsGou, Y. / Liu, Z.C. / Xie, T. / Wang, G.G.
CitationJournal: Colloids Surf B Biointerfaces / Year: 2021
Title: Structure-based rational design of chitosanase CsnMY002 for high yields of chitobiose.
Authors: Li, Y. / Gou, Y. / Liu, Z. / Xie, T. / Wang, G.
History
DepositionMay 21, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 31, 2021Provider: repository / Type: Initial release
Revision 1.1Apr 7, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model
Item: _citation.country / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Chitosanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,3902
Polymers27,4061
Non-polymers9851
Water5,765320
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2350 Å2
ΔGint31 kcal/mol
Surface area11160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.961, 77.921, 79.109
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 Chitosanase


Mass: 27405.547 Da / Num. of mol.: 1 / Mutation: E19A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
Strain: 168 / Gene: csn, BSU26890 / Production host: Escherichia coli (E. coli) / References: UniProt: O07921, chitosanase
#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-(1-4)-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: 984.950 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNb1-4DGlcpNb1-4DGlcpNb1-4DGlcpNb1-4DGlcpNb1-4DGlcpNb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,6,5/[a2122h-1b_1-5_2*N]/1-1-1-1-1-1/a4-b1_b4-c1_c4-d1_d4-e1_e4-f1WURCSPDB2Glycan 1.1.0
[][b-D-GlcpN]{[(4+1)][b-D-GlcpN]{[(4+1)][b-D-GlcpN]{[(4+1)][b-D-GlcpN]{[(4+1)][b-D-GlcpN]{[(4+1)][b-D-GlcpN]{}}}}}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 320 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.64 Å3/Da / Density % sol: 53.42 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M HEPES pH7.5, 0.2M ammonium sulfate and 25%(w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 23, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 1.45→24.98 Å / Num. obs: 51501 / % possible obs: 98.7 % / Redundancy: 12 % / Biso Wilson estimate: 12.7 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.052 / Net I/σ(I): 47.2
Reflection shellResolution: 1.45→1.48 Å / Rmerge(I) obs: 0.133 / Mean I/σ(I) obs: 0.147 / Num. unique obs: 2256 / CC1/2: 0.986

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7C6C

7c6c


Resolution: 1.451→24.978 Å / SU ML: 0.09 / Cross valid method: THROUGHOUT / σ(F): 1.39 / Phase error: 13.42 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.16 2445 4.75 %
Rwork0.136 48992 -
obs0.1371 51437 98.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 46.84 Å2 / Biso mean: 16.2764 Å2 / Biso min: 8.12 Å2
Refinement stepCycle: final / Resolution: 1.451→24.978 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1925 0 67 320 2312
Biso mean--19.31 26.93 -
Num. residues----241
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052074
X-RAY DIFFRACTIONf_angle_d0.8442800
X-RAY DIFFRACTIONf_chiral_restr0.076309
X-RAY DIFFRACTIONf_plane_restr0.006363
X-RAY DIFFRACTIONf_dihedral_angle_d10.611270
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.451-1.48030.16961500.0995248087
1.4803-1.51250.14411420.0998269494
1.5125-1.54760.12771300.0972281697
1.5476-1.58630.15681410.0973286899
1.5863-1.62920.13961330.10232887100
1.6292-1.67710.14631410.1082895100
1.6771-1.73130.14871440.11412886100
1.7313-1.79310.14251580.11792879100
1.7931-1.86490.15381130.12222916100
1.8649-1.94970.16081380.13052927100
1.9497-2.05250.15341520.13822899100
2.0525-2.1810.16451580.13522900100
2.181-2.34930.15421580.13662923100
2.3493-2.58550.15121500.14582929100
2.5855-2.95910.15771470.14882956100
2.9591-3.72620.19431320.14763008100
3.7262-24.9780.16631580.15513129100

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