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- PDB-7c6c: Crystal structure of native chitosanase from Bacillus subtilis MY002 -

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Basic information

Entry
Database: PDB / ID: 7c6c
TitleCrystal structure of native chitosanase from Bacillus subtilis MY002
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
(2S)-2-hydroxybutanedioic acid / Chitosanase
Similarity search - Component
Biological speciesBacillus subtilis subsp. subtilis str. 168 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.258 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)27,5982
Polymers27,4641
Non-polymers1341
Water6,035335
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area11600 Å2
Unit cell
Length a, b, c (Å)47.381, 77.666, 79.211
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: 27463.584 Da / Num. of mol.: 1
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: Chemical ChemComp-LMR / (2S)-2-hydroxybutanedioic acid / L-Malate


Mass: 134.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O5
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 335 / 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: 2.65 Å3/Da / Density % sol: 53.64 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 0.15 M DL-Malic acid pH7.0 and 20% (w/v) PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17B1 / Wavelength: 0.97854 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Nov 22, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97854 Å / Relative weight: 1
ReflectionResolution: 1.258→28.083 Å / Num. obs: 79276 / % possible obs: 99.2 % / Redundancy: 6.4 % / Biso Wilson estimate: 11.76 Å2 / CC1/2: 0.991 / Rmerge(I) obs: 0.068 / Net I/σ(I): 21.9
Reflection shellResolution: 1.258→1.28 Å / Rmerge(I) obs: 0.264 / Mean I/σ(I) obs: 6 / Num. unique obs: 3928 / CC1/2: 0.945 / % possible all: 98.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHASERphasing
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4OLT

4olt


Resolution: 1.258→28.083 Å / SU ML: 0.08 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 14.26 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.166 3859 4.87 %
Rwork0.1497 75342 -
obs0.1506 79201 99.05 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 46.64 Å2 / Biso mean: 17.1443 Å2 / Biso min: 7.51 Å2
Refinement stepCycle: final / Resolution: 1.258→28.083 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1929 0 9 335 2273
Biso mean--31.88 27.12 -
Num. residues----241
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042022
X-RAY DIFFRACTIONf_angle_d0.7682738
X-RAY DIFFRACTIONf_chiral_restr0.076287
X-RAY DIFFRACTIONf_plane_restr0.006367
X-RAY DIFFRACTIONf_dihedral_angle_d4.4642166
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.2581-1.27350.18411150.1532256095
1.2735-1.28960.15531600.13662654100
1.2896-1.30660.15361290.13132676100
1.3066-1.32450.15181260.12222712100
1.3245-1.34340.14731110.12652709100
1.3434-1.36340.14111240.12492696100
1.3634-1.38470.14061270.12112694100
1.3847-1.40740.15931210.12632701100
1.4074-1.43170.14791160.12342715100
1.4317-1.45770.16621340.12422684100
1.4577-1.48580.1461580.12342683100
1.4858-1.51610.15441730.12422674100
1.5161-1.54910.15971410.11912672100
1.5491-1.58510.13371400.12052727100
1.5851-1.62470.13731420.12162684100
1.6247-1.66860.13811480.12592655100
1.6686-1.71770.14831180.13452755100
1.7177-1.77320.15811430.14272714100
1.7732-1.83650.17261400.14972689100
1.8365-1.91010.16971280.15142728100
1.9101-1.9970.19051410.15512721100
1.997-2.10220.16181450.14712728100
2.1022-2.23390.16631590.15012716100
2.2339-2.40630.16031450.15052731100
2.4063-2.64830.16071570.16312743100
2.6483-3.03110.17311510.1661273999
3.0311-3.81730.20061340.1658267495
3.8173-28.0830.16781330.1732250885

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