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- PDB-7cju: Crystal structure of inactive form of chitosanase crystallized by... -

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Basic information

Entry
Database: PDB / ID: 7cju
TitleCrystal structure of inactive form of chitosanase crystallized by ammonium sulfate
ComponentsGlucanase
KeywordsHYDROLASE / enzyme
Function / homology
Function and homology information


Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds / polysaccharide catabolic process / hydrolase activity, hydrolyzing O-glycosyl compounds
Similarity search - Function
Glycoside hydrolase, family 8, conserved site / Glycosyl hydrolases family 8 signature. / Glycoside hydrolase, family 8 / Glycosyl hydrolases family 8 / Six-hairpin glycosidase-like superfamily / Six-hairpin glycosidase superfamily
Similarity search - Domain/homology
Biological speciesBacillus sp. K17-2 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.74 Å
AuthorsGuo, Y. / Qu, L. / Nishida, N. / Hoshino, T.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)18K07138 Japan
CitationJournal: Cryst.Growth Des. / Year: 2021
Title: Electrostatic Potentials around the Proteins Preferably Crystallized by Ammonium Sulfate
Authors: Guo, Y. / Qu, L. / Nishida, N. / Hoshino, T.
History
DepositionJul 14, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 29, 2020Provider: repository / Type: Initial release
Revision 1.1Feb 10, 2021Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Nov 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

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Assembly

Deposited unit
A: Glucanase
B: Glucanase


Theoretical massNumber of molelcules
Total (without water)89,1892
Polymers89,1892
Non-polymers00
Water17,402966
1
A: Glucanase


Theoretical massNumber of molelcules
Total (without water)44,5951
Polymers44,5951
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Glucanase


Theoretical massNumber of molelcules
Total (without water)44,5951
Polymers44,5951
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.949, 92.130, 168.043
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 Glucanase / / chitosanase


Mass: 44594.703 Da / Num. of mol.: 2 / Mutation: S411R,K437T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus sp. K17-2 (bacteria) / Plasmid: pET50b / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3)pLys
References: UniProt: S3JG56, Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 966 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsSequence reference which is derived from Bacillus sp. K17-2 is not available at UNIPROT at the time ...Sequence reference which is derived from Bacillus sp. K17-2 is not available at UNIPROT at the time of data annotation. The sequence reference used (S3JG56) is from a different strain Bacillus cereus BAG1O-3.

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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: 2.51 Å3/Da / Density % sol: 51.06 % / Mosaicity: 0.14 °
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5 / Details: 0.1M Sodium Citrate, 3.4M Ammonium Sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 22, 2020 / Details: mirrors
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.739→48.441 Å / Num. obs: 90669 / % possible obs: 98.9 % / Redundancy: 7.6 % / Biso Wilson estimate: 19.9 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.158 / Rpim(I) all: 0.061 / Rrim(I) all: 0.17 / Net I/σ(I): 8.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.74-1.777.81.3923271242130.5840.5241.4891.693.9
9.52-48.446.30.04241916610.9950.0180.04619.599.6

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Processing

Software
NameVersionClassification
PHENIX1.13refinement
XDSdata reduction
Aimless0.1.27data scaling
PDB_EXTRACT3.25data extraction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdbid 1V5C

1v5c


Resolution: 1.74→48.44 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 17.73 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1903 4527 5 %
Rwork0.1554 86000 -
obs0.1572 90527 98.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 85.77 Å2 / Biso mean: 21.6695 Å2 / Biso min: 6.97 Å2
Refinement stepCycle: final / Resolution: 1.74→48.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6188 0 0 966 7154
Biso mean---33.37 -
Num. residues----776
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.74-1.75830.30961380.2745263393
1.7583-1.7790.28251470.249279096
1.779-1.80070.29551480.2376279899
1.8007-1.82350.26431470.2343280298
1.8235-1.84750.26981500.2149283998
1.8475-1.87280.24691490.2168284399
1.8728-1.89950.25981470.2023279397
1.8995-1.92790.24491500.20442851100
1.9279-1.9580.2211480.1841279998
1.958-1.99010.23971490.1754284099
1.9901-2.02440.23331490.166283698
2.0244-2.06130.21251510.1639285899
2.0613-2.10090.20831490.1585283599
2.1009-2.14380.21531510.1503286199
2.1438-2.19040.18671490.1432284898
2.1904-2.24130.17611500.13752850100
2.2413-2.29740.2041510.1448285998
2.2974-2.35950.16191520.14242881100
2.3595-2.42890.20171490.1432284899
2.4289-2.50730.16721520.1412288699
2.5073-2.59690.20411520.149288999
2.5969-2.70090.18441530.15662906100
2.7009-2.82380.20221520.1678288499
2.8238-2.97270.20871520.1646289499
2.9727-3.15890.18491540.1697292299
3.1589-3.40270.16941540.14692911100
3.4027-3.74510.14811550.12832945100
3.7451-4.28670.14391550.1152957100
4.2867-5.39970.15971590.12313013100
5.3997-48.440.1811650.1669312999

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