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- PDB-7dvb: D335N variant of Bt4394 in complex with 6SO3-NAG-oxazoline interm... -

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Basic information

Entry
Database: PDB / ID: 7dvb
TitleD335N variant of Bt4394 in complex with 6SO3-NAG-oxazoline intermediate
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 / Chem-Q4Z / beta-N-acetylhexosaminidase
Similarity search - Component
Biological speciesBacteroides thetaiotaomicron (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 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 / entity / 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 / _entity.pdbx_mutation / _struct.title
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)248,4359
Polymers247,0014
Non-polymers1,4345
Water8,179454
1
A: Beta-N-acetylhexosaminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,0342
Polymers61,7501
Non-polymers2831
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Beta-N-acetylhexosaminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,0342
Polymers61,7501
Non-polymers2831
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Beta-N-acetylhexosaminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,0342
Polymers61,7501
Non-polymers2831
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Beta-N-acetylhexosaminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,3353
Polymers61,7501
Non-polymers5852
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)82.026, 67.002, 192.803
Angle α, β, γ (deg.)90.000, 94.673, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
32A
42C
53A
63D
74B
84C
95B
105D
116C
126D

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111GLUGLUMETMETAA23 - 5453 - 525
211GLUGLUMETMETBB23 - 5453 - 525
322GLUGLUMETMETAA23 - 5453 - 525
422GLUGLUMETMETCC23 - 5453 - 525
533ILEILEMETMETAA24 - 5454 - 525
633ILEILEMETMETDD24 - 5454 - 525
744GLUGLUMETMETBB23 - 5453 - 525
844GLUGLUMETMETCC23 - 5453 - 525
955ILEILEMETMETBB24 - 5454 - 525
1055ILEILEMETMETDD24 - 5454 - 525
1166ILEILEILEILECC24 - 5444 - 524
1266ILEILEILEILEDD24 - 5444 - 524

NCS ensembles :
IDDetails
1Local NCS retraints between domains: 1 2
2Local NCS retraints between domains: 3 4
3Local NCS retraints between domains: 5 6
4Local NCS retraints between domains: 7 8
5Local NCS retraints between domains: 9 10
6Local NCS retraints between domains: 11 12

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Components

#1: Protein
Beta-N-acetylhexosaminidase


Mass: 61750.297 Da / Num. of mol.: 4 / Mutation: D335N
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: Chemical
ChemComp-Q4Z / [(3~{a}~{R},5~{R},6~{S},7~{R},7~{a}~{R})-2-methyl-6,7-bis(oxidanyl)-5,6,7,7~{a}-tetrahydro-3~{a}~{H}-pyrano[3,2-d][1,3]oxazol-1-ium-5-yl]methyl sulfate


Mass: 283.256 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H13NO8S / Feature type: SUBJECT OF INVESTIGATION
#3: 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.: 1 / 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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 454 / 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: 2.14 Å3/Da / Density % sol: 42.47 %
Crystal growTemperature: 282 K / Method: vapor diffusion, hanging drop
Details: 10 mg/mL protein in the buffer of 25 mM PH 8.0 and 300 mM NaCl was mixed with 0.1 M MES, pH 5.5, 23 % (w/v) PEG 10000 at 1:1 to grow apo crystal. Then the apo was soaked directly with 4MU-6S- ...Details: 10 mg/mL protein in the buffer of 25 mM PH 8.0 and 300 mM NaCl was mixed with 0.1 M MES, pH 5.5, 23 % (w/v) PEG 10000 at 1:1 to grow apo crystal. Then the apo was soaked directly with 4MU-6S-GlcNAc powder for 11 min.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97915 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 12, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.05→19.716 Å / Num. obs: 130228 / % possible obs: 99.2 % / Redundancy: 6.6 % / CC1/2: 0.998 / Rmerge(I) obs: 0.107 / Net I/σ(I): 9.1
Reflection shellResolution: 2.05→2.09 Å / Rmerge(I) obs: 1.024 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 6345 / CC1/2: 0.53

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
HKL-3000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3rcn

3rcn


Resolution: 2.05→19.716 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.927 / WRfactor Rfree: 0.255 / WRfactor Rwork: 0.225 / SU B: 6.297 / SU ML: 0.166 / Average fsc free: 0.8736 / Average fsc work: 0.8846 / Cross valid method: FREE R-VALUE / ESU R: 0.269 / ESU R Free: 0.202 / Details: Hydrogens have not been used
RfactorNum. reflection% reflection
Rfree0.2585 6601 5.069 %
Rwork0.2285 123624 -
all0.23 --
obs-130225 99.159 %
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: 37.394 Å2
Baniso -1Baniso -2Baniso -3
1--0.66 Å2-0 Å2-0.629 Å2
2--1.133 Å20 Å2
3----0.365 Å2
Refinement stepCycle: LAST / Resolution: 2.05→19.716 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16687 0 91 454 17232
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.01217232
X-RAY DIFFRACTIONr_angle_refined_deg0.9441.64323329
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.42252046
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.92522.982929
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.38153047
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.11592
X-RAY DIFFRACTIONr_chiral_restr0.080.22205
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0213100
X-RAY DIFFRACTIONr_nbd_refined0.1910.27396
X-RAY DIFFRACTIONr_nbtor_refined0.3060.211567
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1220.2621
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2640.295
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1310.215
X-RAY DIFFRACTIONr_mcbond_it1.6183.688211
X-RAY DIFFRACTIONr_mcangle_it2.535.51210248
X-RAY DIFFRACTIONr_scbond_it1.8593.7689021
X-RAY DIFFRACTIONr_scangle_it2.9015.57713081
X-RAY DIFFRACTIONr_lrange_it4.57748.28125531
X-RAY DIFFRACTIONr_ncsr_local_group_10.0590.0517624
X-RAY DIFFRACTIONr_ncsr_local_group_20.0650.0517524
X-RAY DIFFRACTIONr_ncsr_local_group_30.0630.0517509
X-RAY DIFFRACTIONr_ncsr_local_group_40.0710.0517549
X-RAY DIFFRACTIONr_ncsr_local_group_50.0670.0517521
X-RAY DIFFRACTIONr_ncsr_local_group_60.0620.0517962
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.058970.05011
12BX-RAY DIFFRACTIONLocal ncs0.058970.05011
23AX-RAY DIFFRACTIONLocal ncs0.065110.0501
24CX-RAY DIFFRACTIONLocal ncs0.065110.0501
35AX-RAY DIFFRACTIONLocal ncs0.063180.0501
36DX-RAY DIFFRACTIONLocal ncs0.063180.0501
47BX-RAY DIFFRACTIONLocal ncs0.071370.0501
48CX-RAY DIFFRACTIONLocal ncs0.071370.0501
59BX-RAY DIFFRACTIONLocal ncs0.067340.0501
510DX-RAY DIFFRACTIONLocal ncs0.067340.0501
611CX-RAY DIFFRACTIONLocal ncs0.061920.05011
612DX-RAY DIFFRACTIONLocal ncs0.061920.05011
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.05-2.1030.3385080.3149026X-RAY DIFFRACTION98.3495
2.103-2.1610.3214390.2998847X-RAY DIFFRACTION98.4939
2.161-2.2240.2954390.2828595X-RAY DIFFRACTION99.1657
2.224-2.2920.3274210.278383X-RAY DIFFRACTION99.2
2.292-2.3670.2884330.268091X-RAY DIFFRACTION99.0587
2.367-2.450.2583940.2587857X-RAY DIFFRACTION99.0873
2.45-2.5430.34280.2567587X-RAY DIFFRACTION99.1833
2.543-2.6460.33880.2567384X-RAY DIFFRACTION99.3227
2.646-2.7640.2843670.2466983X-RAY DIFFRACTION99.3646
2.764-2.8990.3133690.2536712X-RAY DIFFRACTION99.4243
2.899-3.0560.2693510.2456408X-RAY DIFFRACTION99.3824
3.056-3.2410.3043240.2496038X-RAY DIFFRACTION99.7335
3.241-3.4650.2863090.2385722X-RAY DIFFRACTION99.7519
3.742-4.0990.2162440.1974940X-RAY DIFFRACTION99.8844
4.099-4.5830.2172430.1734457X-RAY DIFFRACTION99.8513
4.583-5.2910.1872070.163950X-RAY DIFFRACTION99.8319
5.291-6.4790.222020.1963334X-RAY DIFFRACTION99.9152
6.479-9.1580.2371550.1992626X-RAY DIFFRACTION99.9281

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