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- PDB-8bdp: A GH20 family sulfoglycosidase Bt4394 in complex with NAG-thiazol... -

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Basic information

Entry
Database: PDB / ID: 8bdp
TitleA GH20 family sulfoglycosidase Bt4394 in complex with NAG-thiazoline and sulfite
ComponentsBeta-N-acetylhexosaminidase
KeywordsHYDROLASE / intermediate complex / inhibitor / GH20
Function / homology
Function and homology information


: / glycosaminoglycan metabolic process / beta-N-acetylhexosaminidase activity / beta-N-acetylhexosaminidase / carbohydrate metabolic process / membrane
Similarity search - Function
Beta-hexosaminidase / Glycoside hydrolase family 20, catalytic domain / Glycosyl hydrolase family 20, catalytic domain / Chitobiase/beta-hexosaminidase domain 2-like / Beta-hexosaminidase, bacterial type, N-terminal / Glycosyl hydrolase family 20, domain 2 / Chitobiase; domain 2 / Beta-hexosaminidase-like, domain 2 / Glycosidases / Glycoside hydrolase superfamily ...Beta-hexosaminidase / Glycoside hydrolase family 20, catalytic domain / Glycosyl hydrolase family 20, catalytic domain / Chitobiase/beta-hexosaminidase domain 2-like / Beta-hexosaminidase, bacterial type, N-terminal / Glycosyl hydrolase family 20, domain 2 / Chitobiase; domain 2 / Beta-hexosaminidase-like, domain 2 / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
beta-N-acetylhexosaminidase
Similarity search - Component
Biological speciesBacteroides thetaiotaomicron VPI-5482 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.47 Å
AuthorsZhang, Z. / He, Y. / Jin, Y.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust209057/Z/17/Z United Kingdom
CitationJournal: Acs Catalysis / Year: 2022
Title: Mechanistic and Structural Insights into the Specificity and Biological Functions of Bacterial Sulfoglycosidases
Authors: Zhang, Z. / Dong, M. / Zallot, R. / Blackburn, G.M. / Wang, N. / Wang, C. / Chen, L. / Baumann, P. / Wu, Z. / Wang, Z. / Fan, H. / Roth, C. / Jin, Y. / He, Y.
History
DepositionOct 19, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 11, 2023Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: 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

Downloads & links

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Assembly

Deposited unit
A: Beta-N-acetylhexosaminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,7872
Polymers61,7511
Non-polymers351
Water8,233457
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area130 Å2
ΔGint-12 kcal/mol
Surface area21150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.832, 60.785, 74.223
Angle α, β, γ (deg.)90.000, 107.905, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Beta-N-acetylhexosaminidase


Mass: 61751.281 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides thetaiotaomicron VPI-5482 (bacteria)
Strain: ATCC 29148 / DSM 2079 / JCM 5827 / CCUG 10774 / NCTC 10582 / VPI-5482 / E50
Gene: BT_4394 / Production host: Escherichia coli (E. coli) / Strain (production host): RosettaTM(DE3)pLysS / References: UniProt: Q89ZI3, beta-N-acetylhexosaminidase
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 457 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.32 Å3/Da / Density % sol: 47.06 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: PROTEIN STOCK AT 45 MG/ML IN THE REMARK 280 BUFFER OF 50 MM NAPO4 AND 500 MM NACL IS MIXED WITH THE REMARK 280 PRECIPITANT OF 0.2 M KSCN, 21% PEG3350, 0.1 M BIS-TRIS PROPANE REMARK 280 PH 6. ...Details: PROTEIN STOCK AT 45 MG/ML IN THE REMARK 280 BUFFER OF 50 MM NAPO4 AND 500 MM NACL IS MIXED WITH THE REMARK 280 PRECIPITANT OF 0.2 M KSCN, 21% PEG3350, 0.1 M BIS-TRIS PROPANE REMARK 280 PH 6.5, AT A RATIO OF 1.2: 1.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.979183 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Oct 14, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979183 Å / Relative weight: 1
ReflectionResolution: 1.47→70.63 Å / Num. obs: 91859 / % possible obs: 95.4 % / Redundancy: 1.9 % / CC1/2: 0.997 / Net I/σ(I): 7.8
Reflection shellResolution: 1.47→1.5 Å / Redundancy: 1.9 % / Mean I/σ(I) obs: 1.1 / Num. unique obs: 3088 / CC1/2: 0.624 / % possible all: 65

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Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
xia2data scaling
MOLREPphasing
xia2data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3rcn

3rcn


Resolution: 1.47→70.628 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.963 / WRfactor Rfree: 0.199 / WRfactor Rwork: 0.142 / SU B: 3.759 / SU ML: 0.059 / Average fsc free: 0.9762 / Average fsc work: 0.9901 / Cross valid method: FREE R-VALUE / ESU R: 0.064 / ESU R Free: 0.065
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1823 4641 5.053 %
Rwork0.1299 87199 -
all0.133 --
obs-91840 95.312 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 23.43 Å2
Baniso -1Baniso -2Baniso -3
1-0.883 Å2-0 Å21.716 Å2
2---0.916 Å2-0 Å2
3----0.89 Å2
Refinement stepCycle: LAST / Resolution: 1.47→70.628 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4252 0 1 457 4710
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0124389
X-RAY DIFFRACTIONr_bond_other_d0.0020.0163992
X-RAY DIFFRACTIONr_angle_refined_deg1.5591.6525946
X-RAY DIFFRACTIONr_angle_other_deg0.5471.5659343
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4675530
X-RAY DIFFRACTIONr_dihedral_angle_2_deg5.662523
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.2310780
X-RAY DIFFRACTIONr_dihedral_angle_6_deg16.43710215
X-RAY DIFFRACTIONr_chiral_restr0.0820.2621
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.024962
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02874
X-RAY DIFFRACTIONr_nbd_refined0.2230.2788
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1860.23664
X-RAY DIFFRACTIONr_nbtor_refined0.180.22091
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0780.22129
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.150.2301
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1260.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1620.213
X-RAY DIFFRACTIONr_nbd_other0.1970.242
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1590.224
X-RAY DIFFRACTIONr_mcbond_it3.5492.2472105
X-RAY DIFFRACTIONr_mcbond_other3.5492.2472105
X-RAY DIFFRACTIONr_mcangle_it4.0193.3942634
X-RAY DIFFRACTIONr_mcangle_other4.0233.3942635
X-RAY DIFFRACTIONr_scbond_it5.3262.6872284
X-RAY DIFFRACTIONr_scbond_other5.3262.6882285
X-RAY DIFFRACTIONr_scangle_it5.9693.843310
X-RAY DIFFRACTIONr_scangle_other5.9683.8413311
X-RAY DIFFRACTIONr_lrange_it5.58734.2045040
X-RAY DIFFRACTIONr_lrange_other5.48132.6414929
X-RAY DIFFRACTIONr_rigid_bond_restr5.06338381
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.47-1.5080.2612270.24444600.24570860.960.97566.14450.252
1.508-1.5490.2462800.21751530.21969180.9640.98278.53430.22
1.549-1.5940.2623310.19459550.19767280.9670.98593.43040.192
1.594-1.6430.2393610.16661760.1765370.9720.991000.163
1.643-1.6970.2222990.15159970.15462960.9760.9921000.145
1.697-1.7570.2312800.14458490.14861300.9710.99199.98370.136
1.757-1.8230.1932990.12856140.13159230.9830.99399.83120.12
1.823-1.8970.1892830.10654140.1156970.980.9951000.099
1.897-1.9820.2132670.11352090.11854760.9730.9941000.107
1.982-2.0780.172780.10549170.10951950.9830.9951000.101
2.078-2.1910.1682630.11347290.11650080.9830.99499.68050.111
2.191-2.3230.1712670.1144220.11446930.9810.99399.91480.11
2.323-2.4840.1682090.10241930.10544090.9820.99499.84120.105
2.484-2.6820.1571890.10439650.10641650.9850.99499.73590.109
2.682-2.9380.1651980.11635570.11937930.9830.99298.99820.125
2.938-3.2840.1741730.12632560.12834380.980.99199.73820.139
3.284-3.7910.1681570.12729010.12930670.9830.9999.70660.147
3.791-4.6390.1331270.11624390.11725910.9910.99299.03510.146
4.639-6.5470.187950.15119040.15320120.9860.9999.35390.189
6.547-70.6280.262580.22910880.23111670.9330.95898.20050.536

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