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- PDB-6inx: Structural insights into a novel glycoside hydrolase family 18 N-... -

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Basic information

Entry
Database: PDB / ID: 6inx
TitleStructural insights into a novel glycoside hydrolase family 18 N-acetylglucosaminidase from Paenibacillus barengoltzii
ComponentsN-acetylglucosaminidase
KeywordsHYDROLASE / N-acetylglucosaminidase / GH18 / STRUCTURAL PROTEIN
Function / homology
Function and homology information


beta-N-acetylhexosaminidase activity / beta-N-acetylhexosaminidase / N-acetyl-beta-D-galactosaminidase activity / chitin binding / carbohydrate metabolic process
Similarity search - Function
Chitinase A; domain 3 - #10 / Glycosyl hydrolases family 18 (GH18) active site / Glycosyl hydrolases family 18 (GH18) active site signature. / Chitinase insertion domain superfamily / Chitinase II / Glyco_18 / Glycoside hydrolase family 18, catalytic domain / Glycosyl hydrolases family 18 / Chitinase A; domain 3 / Glycosidases ...Chitinase A; domain 3 - #10 / Glycosyl hydrolases family 18 (GH18) active site / Glycosyl hydrolases family 18 (GH18) active site signature. / Chitinase insertion domain superfamily / Chitinase II / Glyco_18 / Glycoside hydrolase family 18, catalytic domain / Glycosyl hydrolases family 18 / Chitinase A; domain 3 / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Roll / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Beta-N-acetylglucosaminidase
Similarity search - Component
Biological speciesPaenibacillus barengoltzii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.429 Å
AuthorsJiang, Z. / Ma, J. / Huang, P.
CitationJournal: To Be Published
Title: Structural insights into a novel glycoside hydrolase family 18 N-acetylglucosaminidase from Paenibacillus barengoltzii
Authors: Jiang, Z.Q. / Ma, J.W. / Huang, P.
History
DepositionOct 28, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 30, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 22, 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

Downloads & links

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Assembly

Deposited unit
A: N-acetylglucosaminidase


Theoretical massNumber of molelcules
Total (without water)39,0321
Polymers39,0321
Non-polymers00
Water6,593366
1
A: N-acetylglucosaminidase

A: N-acetylglucosaminidase


Theoretical massNumber of molelcules
Total (without water)78,0632
Polymers78,0632
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Buried area2060 Å2
ΔGint-16 kcal/mol
Surface area25480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.890, 76.300, 61.440
Angle α, β, γ (deg.)90.00, 126.79, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-742-

HOH

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Components

#1: Protein N-acetylglucosaminidase


Mass: 39031.645 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Paenibacillus barengoltzii (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: A0A482G4C5*PLUS, mannosyl-glycoprotein endo-beta-N-acetylglucosaminidase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 366 / 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: 2.2 Å3/Da / Density % sol: 44.12 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.07M sodium acetate trihydrate, 5.6% w/v polyethylene glycol 4000, 30% v/v glycerol

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: 90-100 / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 R CdTe 300K / Detector: PIXEL / Date: Jan 10, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.429→38.15 Å / Num. obs: 81007 / % possible obs: 97.1 % / Redundancy: 6.5 % / Net I/σ(I): 9.023
Reflection shellResolution: 1.429→1.429 Å / Rmerge(I) obs: 0.036 / CC1/2: 0.997 / Rpim(I) all: 0.016

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Processing

Software
NameVersionClassification
PHENIX(dev_2474: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXmodel building
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5GZU

5gzu


Resolution: 1.429→38.15 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 0.88 / Phase error: 21.58
RfactorNum. reflection% reflection
Rfree0.203 3241 5.25 %
Rwork0.181 --
obs0.1822 81006 97.33 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.429→38.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2702 0 0 366 3068
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052766
X-RAY DIFFRACTIONf_angle_d0.8413748
X-RAY DIFFRACTIONf_dihedral_angle_d3.5381001
X-RAY DIFFRACTIONf_chiral_restr0.084393
X-RAY DIFFRACTIONf_plane_restr0.005491
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4293-1.45070.30871120.32332300X-RAY DIFFRACTION90
1.4507-1.47330.25081270.29022531X-RAY DIFFRACTION97
1.4733-1.49750.29181630.26042583X-RAY DIFFRACTION98
1.4975-1.52330.28011680.24892503X-RAY DIFFRACTION98
1.5233-1.5510.23131710.2252520X-RAY DIFFRACTION98
1.551-1.58080.22831570.21012545X-RAY DIFFRACTION98
1.5808-1.61310.22551340.19952532X-RAY DIFFRACTION98
1.6131-1.64820.23711360.18932529X-RAY DIFFRACTION98
1.6482-1.68650.23871260.19182569X-RAY DIFFRACTION98
1.6865-1.72870.22911130.1842563X-RAY DIFFRACTION97
1.7287-1.77540.19911380.19272523X-RAY DIFFRACTION96
1.7754-1.82770.23441490.19422551X-RAY DIFFRACTION98
1.8277-1.88670.21881530.18112567X-RAY DIFFRACTION99
1.8867-1.95410.2261590.17132566X-RAY DIFFRACTION99
1.9541-2.03230.19271430.17292610X-RAY DIFFRACTION99
2.0323-2.12480.19661350.16612595X-RAY DIFFRACTION99
2.1248-2.23680.19181340.16592574X-RAY DIFFRACTION99
2.2368-2.3770.17031010.16592609X-RAY DIFFRACTION98
2.377-2.56050.19991250.17182496X-RAY DIFFRACTION95
2.5605-2.8180.18421220.16832637X-RAY DIFFRACTION99
2.818-3.22560.18061620.16382583X-RAY DIFFRACTION99
3.2256-4.06320.17021590.15482520X-RAY DIFFRACTION97
4.0632-38.16360.20551540.18632441X-RAY DIFFRACTION91

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