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- PDB-7dva: Structure of wild type Bt4394, a GH20 family sulfoglycosidase, in... -

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Basic information

Entry
Database: PDB / ID: 7dva
TitleStructure of wild type Bt4394, a GH20 family sulfoglycosidase, in complex with 6S-GlcNAc
ComponentsBeta-N-acetylhexosaminidase
KeywordsHYDROLASE / GH20 / Complex
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
Chem-NGS / beta-N-acetylhexosaminidase
Similarity search - Component
Biological speciesBacteroides thetaiotaomicron (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsZhang, Z. / He, Y. / Jin, Y.
Funding support United Kingdom, China, 2items
OrganizationGrant numberCountry
Wellcome Trust209057/Z/17/Z United Kingdom
National Natural Science Foundation of China (NSFC)31400663 China
CitationJournal: Acs Catalysis / Year: 2023
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
DepositionJan 13, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 19, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 18, 2023Group: Database references / Derived calculations / Structure summary
Category: atom_type / citation ...atom_type / citation / citation_author / struct
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _struct.title
Revision 1.2Nov 29, 2023Group: 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

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Assembly

Deposited unit
B: Beta-N-acetylhexosaminidase
A: Beta-N-acetylhexosaminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,5669
Polymers123,5032
Non-polymers1,0637
Water10,196566
1
B: Beta-N-acetylhexosaminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,2374
Polymers61,7511
Non-polymers4853
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area200 Å2
ΔGint-0 kcal/mol
Surface area20800 Å2
MethodPISA
2
A: Beta-N-acetylhexosaminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,3295
Polymers61,7511
Non-polymers5784
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area200 Å2
ΔGint-0 kcal/mol
Surface area20850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.500, 125.596, 84.640
Angle α, β, γ (deg.)90.000, 90.631, 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.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides thetaiotaomicron (bacteria)
Production host: Escherichia coli (E. coli)
References: UniProt: A0A0P0FIE8, beta-N-acetylhexosaminidase
#2: Sugar ChemComp-NGS / 2-acetamido-2-deoxy-6-O-sulfo-beta-D-glucopyranose / 2-(acetylamino)-2-deoxy-6-O-sulfo-beta-D-glucopyranose / N-ACETYL-D-GLUCOSAMINE-6-SULFATE / N-acetyl-6-O-sulfo-beta-D-glucosamine / 2-acetamido-2-deoxy-6-O-sulfo-beta-D-glucose / 2-acetamido-2-deoxy-6-O-sulfo-D-glucose / 2-acetamido-2-deoxy-6-O-sulfo-glucose


Type: D-saccharide, beta linking / Mass: 301.271 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H15NO9S / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGlcpNAc[6S]bCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-6-sulfo-b-D-glucopyranoseCOMMON NAMEGMML 1.0
b-D-GlcpNAc6SO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 566 / 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: 2.13 Å3/Da / Density % sol: 42.26 %
Crystal growTemperature: 282 K / Method: vapor diffusion, sitting drop
Details: 10 mM of 4MU-6S-GlcNAc with 10 mg/mL protein in the buffer of 25 mM PH 8.0, =300 mM NaCl was mixed with 0.1 M BICINE, pH 8.5, 20 % (w/v) PEG 10000 at 1:1 to carry on co-crystallization.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.979191 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 28, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979191 Å / Relative weight: 1
ReflectionResolution: 1.55→70.19 Å / Num. obs: 145268 / % possible obs: 97.4 % / Redundancy: 6.8 % / CC1/2: 0.996 / Rmerge(I) obs: 0.097 / Net I/σ(I): 11.5
Reflection shellResolution: 1.55→1.58 Å / Rmerge(I) obs: 1.005 / Mean I/σ(I) obs: 2 / Num. unique obs: 7086 / CC1/2: 0.584

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3rcn

3rcn


Resolution: 1.55→50.483 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.965 / WRfactor Rfree: 0.195 / WRfactor Rwork: 0.147 / SU B: 3.681 / SU ML: 0.057 / Average fsc free: 0.9221 / Average fsc work: 0.9352 / Cross valid method: FREE R-VALUE / ESU R: 0.092 / ESU R Free: 0.076
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1844 7467 5.142 %
Rwork0.1417 137760 -
all0.144 --
obs-145227 97.224 %
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: 22.979 Å2
Baniso -1Baniso -2Baniso -3
1--0.449 Å2-0 Å20.328 Å2
2--1.723 Å20 Å2
3----1.281 Å2
Refinement stepCycle: LAST / Resolution: 1.55→50.483 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8495 0 68 566 9129
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0128856
X-RAY DIFFRACTIONr_angle_refined_deg1.2171.64711997
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.46651061
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.20723.172476
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.863151561
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4141546
X-RAY DIFFRACTIONr_chiral_restr0.0920.21129
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.026808
X-RAY DIFFRACTIONr_nbd_refined0.2020.24175
X-RAY DIFFRACTIONr_nbtor_refined0.3150.25983
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1130.2560
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.240.275
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1310.221
X-RAY DIFFRACTIONr_mcbond_it1.7621.9634221
X-RAY DIFFRACTIONr_mcangle_it2.2842.9595283
X-RAY DIFFRACTIONr_scbond_it2.6252.3444635
X-RAY DIFFRACTIONr_scangle_it3.0693.3626712
X-RAY DIFFRACTIONr_lrange_it3.4428.0413768
X-RAY DIFFRACTIONr_rigid_bond_restr1.46738856
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.55-1.590.3225120.28110063X-RAY DIFFRACTION95.8662
1.59-1.6340.3235280.2569744X-RAY DIFFRACTION95.9193
1.634-1.6810.2535420.1889467X-RAY DIFFRACTION95.8349
1.681-1.7330.2354920.1599287X-RAY DIFFRACTION96.4303
1.733-1.790.2044750.1329060X-RAY DIFFRACTION96.7529
1.79-1.8520.2034690.1218764X-RAY DIFFRACTION97.0465
1.852-1.9220.2094460.1478454X-RAY DIFFRACTION96.8971
1.922-2.0010.184360.1268149X-RAY DIFFRACTION97.1484
2.001-2.090.1934090.1257854X-RAY DIFFRACTION97.487
2.09-2.1920.174110.1197541X-RAY DIFFRACTION97.9672
2.192-2.310.1813940.1237121X-RAY DIFFRACTION97.6228
2.31-2.450.1773860.1236802X-RAY DIFFRACTION98.1297
2.45-2.620.1793300.1286411X-RAY DIFFRACTION98.0224
2.62-2.8290.1873610.1435943X-RAY DIFFRACTION99.0261
2.829-3.0990.1872940.1425513X-RAY DIFFRACTION98.2905
3.099-3.4650.1672690.1345008X-RAY DIFFRACTION99.0428
3.465-40.1622410.1294351X-RAY DIFFRACTION97.5776
4-4.8980.1592080.143751X-RAY DIFFRACTION99.0245

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