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- PDB-6yhh: X-ray Structure of Flavobacterium johnsoniae chitobiase (FjGH20) -

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Basic information

Entry
Database: PDB / ID: 6yhh
TitleX-ray Structure of Flavobacterium johnsoniae chitobiase (FjGH20)
ComponentsBeta-N-acetylglucosaminidase-like protein Glycoside hydrolase family 20
KeywordsHYDROLASE / bacterial chitin metabolism / chitin degradation / N-acetylglucosaminidase / GH20
Function / homology
Function and homology information


beta-N-acetylhexosaminidase / beta-N-acetylhexosaminidase activity / N-acetyl-beta-D-galactosaminidase activity / carbohydrate metabolic process
Similarity search - Function
Beta-hexosaminidase / Glycoside hydrolase family 20, catalytic domain / Glycosyl hydrolase family 20, catalytic domain / Beta-hexosaminidase, bacterial type, N-terminal / Glycosyl hydrolase family 20, domain 2 / Beta-hexosaminidase-like, domain 2 / Glycoside hydrolase superfamily
Similarity search - Domain/homology
Beta-N-acetylhexosaminidase
Similarity search - Component
Biological speciesFlavobacterium johnsoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsMazurkewich, S. / Helland, R. / MacKenzie, A. / Eijsink, V.G.H. / Pope, P.B. / Branden, G. / Larsbrink, J.
Funding support Sweden, Norway, 5items
OrganizationGrant numberCountry
Knut and Alice Wallenberg Foundation Sweden
Norwegian Research Council247732 Norway
Norwegian Research Council214042 Norway
Norwegian Research Council221568 Norway
European Research Council (ERC)336355
CitationJournal: Sci Rep / Year: 2020
Title: Structural insights of the enzymes from the chitin utilization locus of Flavobacterium johnsoniae.
Authors: Mazurkewich, S. / Helland, R. / Mackenzie, A. / Eijsink, V.G.H. / Pope, P.B. / Branden, G. / Larsbrink, J.
History
DepositionMar 30, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 2, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: 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

Downloads & links

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Assembly

Deposited unit
A: Beta-N-acetylglucosaminidase-like protein Glycoside hydrolase family 20
B: Beta-N-acetylglucosaminidase-like protein Glycoside hydrolase family 20
hetero molecules


Theoretical massNumber of molelcules
Total (without water)151,8295
Polymers151,4922
Non-polymers3363
Water27,8151544
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5020 Å2
ΔGint-9 kcal/mol
Surface area45900 Å2
Unit cell
Length a, b, c (Å)75.986, 124.547, 151.587
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 Beta-N-acetylglucosaminidase-like protein Glycoside hydrolase family 20


Mass: 75746.195 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Flavobacterium johnsoniae (strain ATCC 17061 / DSM 2064 / UW101) (bacteria)
Strain: ATCC 17061 / DSM 2064 / UW101 / Gene: Fjoh_4556 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A5FB64, beta-N-acetylhexosaminidase
#2: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#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
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1544 / 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: 2.37 Å3/Da / Density % sol: 48 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 14% PEGMME 5K, 0.1 M Na-Malonate

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Data collection

DiffractionMean temperature: 120 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.918409 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Apr 14, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918409 Å / Relative weight: 1
ReflectionResolution: 1.7→49 Å / Num. obs: 158136 / % possible obs: 99.9 % / Redundancy: 6.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.077 / Rpim(I) all: 0.032 / Rrim(I) all: 0.084 / Net I/σ(I): 17.2
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
1.7-1.734.70.443565276370.8680.2230.4963.298.4
9.31-48.165.70.024627010960.9990.0110.02650.498.7

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Processing

Software
NameVersionClassification
Aimless0.5.8data scaling
REFMAC5.8.0073refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
Auto-Rickshawphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1NOW

1now


Resolution: 1.7→49 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.955 / SU B: 1.672 / SU ML: 0.055 / SU R Cruickshank DPI: 0.0838 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.084 / ESU R Free: 0.085
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.175 7814 4.9 %RANDOM
Rwork0.1427 ---
obs0.1443 150222 99.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 65.71 Å2 / Biso mean: 15.113 Å2 / Biso min: 6.33 Å2
Baniso -1Baniso -2Baniso -3
1-1.35 Å2-0 Å20 Å2
2---1.11 Å2-0 Å2
3----0.24 Å2
Refine analyzeLuzzati coordinate error obs: 0.15 Å
Refinement stepCycle: final / Resolution: 1.7→49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10208 0 22 1544 11774
Biso mean--18.24 23.91 -
Num. residues----1310
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.01910540
X-RAY DIFFRACTIONr_bond_other_d0.0010.029906
X-RAY DIFFRACTIONr_angle_refined_deg1.9451.95414329
X-RAY DIFFRACTIONr_angle_other_deg0.952322767
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.351328
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.45224.937474
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.555151758
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.4291546
X-RAY DIFFRACTIONr_chiral_restr0.1360.21612
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.02112041
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022397
LS refinement shellResolution: 1.7→1.744 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.241 521 -
Rwork0.196 10868 -
all-11389 -
obs--98.67 %

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