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- PDB-6k5j: Structure of a glycoside hydrolase family 3 beta-N-acetylglucosam... -

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Basic information

Entry
Database: PDB / ID: 6k5j
TitleStructure of a glycoside hydrolase family 3 beta-N-acetylglucosaminidase from Paenibacillus sp. str. FPU-7
ComponentsGH3 beta-N-acetylglucosaminidase
KeywordsHYDROLASE / glucosidase
Function / homologyGlycoside hydrolase, family 3, N-terminal domain / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Function and homology information
Biological speciesPaenibacillaceae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.903 Å
AuthorsItoh, T. / Araki, T. / Nishiyama, T. / Hibi, T. / Kimoto, H.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science16K08114, 19K06340 Japan
CitationJournal: J.Biochem. / Year: 2019
Title: Structural and functional characterization of a glycoside hydrolase family 3 beta-N-acetylglucosaminidase from Paenibacillus sp. str. FPU-7.
Authors: Itoh, T. / Araki, T. / Nishiyama, T. / Hibi, T. / Kimoto, H.
History
DepositionMay 29, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 25, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 11, 2019Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _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: GH3 beta-N-acetylglucosaminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,3643
Polymers57,0501
Non-polymers3132
Water8,071448
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, monomer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)84.230, 84.230, 157.805
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein GH3 beta-N-acetylglucosaminidase


Mass: 57050.461 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Paenibacillaceae (bacteria) / Variant: FPU-7 / Production host: Escherichia coli BL21 (bacteria) / References: beta-N-acetylhexosaminidase
#2: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 448 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsThe N-teminal residues, Met1-Lys9, are missing. MNHKVHHHHHHIEGRHMELGTLEGS at N-teminus derived from ...The N-teminal residues, Met1-Lys9, are missing. MNHKVHHHHHHIEGRHMELGTLEGS at N-teminus derived from pCold I vector are also missing. Cys269 is oxidized to sulfinic acid (CSD).

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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: 2.5 Å3/Da / Density % sol: 50.73 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 15% (w/v) PEG8000, 0.2 M calcium acetate, 0.1 M 4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid, pH 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 18, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→47.5 Å / Num. obs: 45405 / % possible obs: 100 % / Redundancy: 12.7 % / Biso Wilson estimate: 32.1 Å2 / Rmerge(I) obs: 0.101 / Net I/σ(I): 19.4
Reflection shellResolution: 1.9→1.95 Å / Redundancy: 12.8 % / Rmerge(I) obs: 0.967 / Mean I/σ(I) obs: 2.9 / Num. unique obs: 2994 / % possible all: 99.5

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3BMX

3bmx


Resolution: 1.903→44.616 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 17.63
RfactorNum. reflection% reflection
Rfree0.2039 2270 5.01 %
Rwork0.1615 --
obs0.1636 45304 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 65.74 Å2 / Biso mean: 27.1618 Å2 / Biso min: 14.5 Å2
Refinement stepCycle: final / Resolution: 1.903→44.616 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3942 0 21 448 4411
Biso mean--24.78 35.79 -
Num. residues----526
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 16

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9031-1.94440.26571240.207226532777100
1.9444-1.98970.24071570.191626152772100
1.9897-2.03940.19631270.174826442771100
2.0394-2.09460.20971440.173926452789100
2.0946-2.15620.23561210.160526832804100
2.1562-2.22580.20161300.16226552785100
2.2258-2.30540.20881680.156226172785100
2.3054-2.39770.18191260.161326772803100
2.3977-2.50680.19461280.154426932821100
2.5068-2.63890.18091570.159426672824100
2.6389-2.80420.20381550.159526662821100
2.8042-3.02070.19751330.168626962829100
3.0207-3.32460.2651290.16327282857100
3.3246-3.80540.17581600.148227192879100
3.8054-4.79360.19331370.136927662903100
4.7936-44.62840.21041740.18392910308499

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