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- PDB-7xgq: Crystal structure of chitosanase crystallized by ammonium sulfate... -

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Basic information

Entry
Database: PDB / ID: 7xgq
TitleCrystal structure of chitosanase crystallized by ammonium sulfate with glycan
Componentschitosanase
KeywordsHYDROLASE / glucanase
Biological speciesBacillus sp. K17-2 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsGuo, Y. / Hoshino, T.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)21K07050 Japan
CitationJournal: Cryst.Growth Des. / Year: 2022
Title: Influence of Glycan Agents on Protein Crystallization with Ammonium Sulfate
Authors: Guo, Y. / Hoshino, T.
History
DepositionApr 5, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 20, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 2, 2022Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: chitosanase
B: chitosanase


Theoretical massNumber of molelcules
Total (without water)89,1892
Polymers89,1892
Non-polymers00
Water10,755597
1
A: chitosanase


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


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)57.422, 92.110, 175.169
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: 44594.703 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Sequence used in this structure is identical with the sequence of chain A from structure 7CJU.
Source: (gene. exp.) Bacillus sp. K17-2 (bacteria) / Plasmid: pET50b / Production host: Escherichia coli (E. coli) / Variant (production host): Rosetta(DE3)pLys / References: chitosanase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 597 / Source method: isolated from a natural source / Formula: H2O

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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: 2.6 Å3/Da / Density % sol: 52.64 % / Mosaicity: 0.22 °
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 0.1M Sodium Citrate, 3.4M Ammonium Sulfate, 5%(v/v) tri[(O-beta-D-glucopyranosyl)ethyloxy]cholane

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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: 1.5→48.73 Å / Num. obs: 142580 / % possible obs: 95.7 % / Redundancy: 6.8 % / CC1/2: 0.991 / Rmerge(I) obs: 0.056 / Rpim(I) all: 0.023 / Rrim(I) all: 0.061 / Net I/σ(I): 18.8
Reflection shellResolution: 1.5→1.53 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.975 / Num. unique obs: 6809 / CC1/2: 0.559 / Rpim(I) all: 0.397 / Rrim(I) all: 1.055 / % possible all: 93.1

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Processing

Software
NameVersionClassification
PHENIX1.13refinement
XDSdata reduction
Aimless0.1.27data scaling
PDB_EXTRACT3.27data extraction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7CJU

7cju


Resolution: 1.5→48.729 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.92 / Phase error: 22.19 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.21 7125 4.99 %
Rwork0.1818 --
obs0.1831 142495 94.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 69.67 Å2 / Biso mean: 22.4989 Å2 / Biso min: 9.27 Å2
Refinement stepCycle: final / Resolution: 1.5→48.729 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6183 0 0 597 6780
Biso mean---29.72 -
Num. residues----775
LS refinement shellResolution: 1.5→1.53 Å
RfactorNum. reflection% reflection
Rfree0.21 --
Rwork0.1818 --
all-46665 -
obs-6809 93.1 %

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