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- PDB-9x1i: Structure of endo-beta-N-acetylglucosaminidase HS -

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Basic information

Entry
Database: PDB / ID: 9x1i
TitleStructure of endo-beta-N-acetylglucosaminidase HS
ComponentsEndo-beta-N-acetylglucosaminidase HS
KeywordsHYDROLASE / endo-beta-N-acetylglucosaminidase
Function / homology:
Function and homology information
Biological specieshuman oral metagenome (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.81 Å
AuthorsKurauchi, I. / Okura, K. / Hosokawa, C. / Ito, K. / Miyahra, I.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2026
Title: Crystal structure of endo-beta-N-acetylglucosaminidase HS alpha.
Authors: Kurauchi, I. / Okura, K. / Hosokawa, C. / Ito, K. / Miyahara, I.
History
DepositionOct 2, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 18, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Endo-beta-N-acetylglucosaminidase HS
B: Endo-beta-N-acetylglucosaminidase HS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)218,59511
Polymers217,8642
Non-polymers7319
Water42,8222377
1
A: Endo-beta-N-acetylglucosaminidase HS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,3436
Polymers108,9321
Non-polymers4115
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area35800 Å2
MethodPISA
2
B: Endo-beta-N-acetylglucosaminidase HS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,2515
Polymers108,9321
Non-polymers3194
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area230 Å2
ΔGint-18 kcal/mol
Surface area35670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.927, 135.567, 238.865
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab

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Components

#1: Protein Endo-beta-N-acetylglucosaminidase HS


Mass: 108932.008 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: N-terminal truncation of 29 residues / Source: (gene. exp.) human oral metagenome (others) / Production host: Escherichia coli (E. coli)
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2377 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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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: 52.74 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 2.0M Ammonium sulfate, 0.1M Bis-Tris-HCl buffer / PH range: 5.0-6.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Jun 15, 2023
Details: Collimating mirror (19.2 m): Rhodium coated silicon single crystal (Flat shaped, 1000 mm (L) x 80 mm (W) x 70 mm (T)) with 3.5 mrad glancing angle Monochromator (20.8 m): Numerical link type ...Details: Collimating mirror (19.2 m): Rhodium coated silicon single crystal (Flat shaped, 1000 mm (L) x 80 mm (W) x 70 mm (T)) with 3.5 mrad glancing angle Monochromator (20.8 m): Numerical link type Si(111) double crystal monochromator, liquid nitrogen cooling Focusing mirror (22.9 m): Rhodium coated SiO2 (Troidal, 1000 mm (L) x 100 mm (W) x 65 mm (T)) with 3.5 mrad glancing angle
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→49.7 Å / Num. obs: 212496 / % possible obs: 99.8 % / Redundancy: 6.6 % / Biso Wilson estimate: 21.21 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.085 / Rpim(I) all: 0.036 / Rrim(I) all: 0.093 / Χ2: 0.98 / Net I/σ(I): 12.9
Reflection shellResolution: 1.81→1.84 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.686 / Mean I/σ(I) obs: 2.8 / Num. unique obs: 10040 / CC1/2: 0.896 / Rpim(I) all: 0.292 / Rrim(I) all: 0.748 / Χ2: 0.92 / % possible all: 96.4

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimlessdata scaling
Cootmodel building
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.81→39.05 Å / SU ML: 0.2142 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.2977
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2421 10601 5 %
Rwork0.1959 201625 -
obs0.1981 212226 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 27.43 Å2
Refinement stepCycle: LAST / Resolution: 1.81→39.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15044 0 42 2377 17463
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006715405
X-RAY DIFFRACTIONf_angle_d0.880520898
X-RAY DIFFRACTIONf_chiral_restr0.05552240
X-RAY DIFFRACTIONf_plane_restr0.00712755
X-RAY DIFFRACTIONf_dihedral_angle_d6.63512107
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.81-1.830.33193560.29256439X-RAY DIFFRACTION97.1
1.83-1.850.29833420.26326674X-RAY DIFFRACTION99.89
1.85-1.870.30233580.24536590X-RAY DIFFRACTION99.84
1.87-1.90.29363360.23926714X-RAY DIFFRACTION99.94
1.9-1.920.29553280.23536670X-RAY DIFFRACTION99.9
1.92-1.950.28463930.23436697X-RAY DIFFRACTION99.96
1.95-1.980.27563460.22526605X-RAY DIFFRACTION99.84
1.98-2.010.25593650.21176665X-RAY DIFFRACTION99.96
2.01-2.040.26933730.21456654X-RAY DIFFRACTION99.86
2.04-2.070.27363300.21286699X-RAY DIFFRACTION99.94
2.07-2.110.27163460.20566683X-RAY DIFFRACTION99.83
2.11-2.150.26863730.20856652X-RAY DIFFRACTION99.94
2.15-2.190.25993540.20346694X-RAY DIFFRACTION99.93
2.19-2.230.25993380.20126696X-RAY DIFFRACTION99.91
2.23-2.280.24343410.19466681X-RAY DIFFRACTION99.97
2.28-2.330.24623480.19636737X-RAY DIFFRACTION99.9
2.33-2.390.2623710.20016714X-RAY DIFFRACTION99.97
2.39-2.460.2463500.1956673X-RAY DIFFRACTION99.97
2.46-2.530.2513550.20276699X-RAY DIFFRACTION99.96
2.53-2.610.26383860.2046702X-RAY DIFFRACTION99.97
2.61-2.70.26373470.20066718X-RAY DIFFRACTION99.96
2.7-2.810.24493560.19976732X-RAY DIFFRACTION99.97
2.81-2.940.27483350.19956769X-RAY DIFFRACTION99.94
2.94-3.090.2533540.20156777X-RAY DIFFRACTION99.89
3.09-3.290.24113560.18876780X-RAY DIFFRACTION99.99
3.29-3.540.22523600.17996772X-RAY DIFFRACTION99.9
3.54-3.90.21713320.17286827X-RAY DIFFRACTION99.82
3.9-4.460.18453350.16196871X-RAY DIFFRACTION99.92
4.46-5.620.18383680.16766893X-RAY DIFFRACTION99.66
5.62-39.050.23683690.20847148X-RAY DIFFRACTION99.37

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