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- PDB-8u48: Crystal structure of Bacteroides thetaiotamicron BT1285 D161A-E16... -

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Basic information

Entry
Database: PDB / ID: 8u48
TitleCrystal structure of Bacteroides thetaiotamicron BT1285 D161A-E163A inactive Endoglycosidase in complex with high-mannose N-glycan (Man9GlcNAc2) substrate
ComponentsEndo-beta-N-acetylglucosaminidase
KeywordsCARBOHYDRATE / Inactive Endoglycosidase / Artificial Lectin / High-Mannose specific / Bacteroides / GH18 family
Function / homology
Function and homology information


mannosyl-glycoprotein endo-beta-N-acetylglucosaminidase activity / carbohydrate metabolic process / extracellular region / metal ion binding
Similarity search - Function
Endo-beta-N-acetylglucosaminidase / Glycosyl hydrolases family 18 (GH18) active site / Glycosyl hydrolases family 18 (GH18) active site signature. / Glycosyl hydrolases family 18 / Glycosyl hydrolases family 18 (GH18) domain profile. / Glycoside hydrolase family 18, catalytic domain / Prokaryotic membrane lipoprotein lipid attachment site profile. / Glycoside hydrolase superfamily
Similarity search - Domain/homology
PHOSPHATE ION / Endo-beta-N-acetylglucosaminidase
Similarity search - Component
Biological speciesBacteroides thetaiotaomicron VPI-5482 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsSastre, D.E. / Sultana, N. / Navarro, M.V.A.S. / Sundberg, E.J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1R01GM148075-01A1 United States
CitationJournal: Nat Commun / Year: 2024
Title: Human gut microbes express functionally distinct endoglycosidases to metabolize the same N-glycan substrate.
Authors: Sastre, D.E. / Sultana, N. / V A S Navarro, M. / Huliciak, M. / Du, J. / Cifuente, J.O. / Flowers, M. / Liu, X. / Lollar, P. / Trastoy, B. / Guerin, M.E. / Sundberg, E.J.
History
DepositionSep 9, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 29, 2024Provider: repository / Type: Initial release
Revision 1.1Jun 26, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)64,8548
Polymers60,7072
Non-polymers4,1476
Water11,620645
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.919, 71.260, 80.487
Angle α, β, γ (deg.)90.00, 94.63, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Endo-beta-N-acetylglucosaminidase


Mass: 30353.545 Da / Num. of mol.: 2 / Mutation: D161A, E163A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides thetaiotaomicron VPI-5482 (bacteria)
Gene: BT_1285 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q8A889
#2: Polysaccharide alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1883.668 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-2DManpa1-2DManpa1-3[DManpa1-2DManpa1-3[DManpa1-2DManpa1-6]DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,11,10/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3-3-3-3-3-3/a4-b1_b4-c1_c3-d1_c6-g1_d2-e1_e2-f1_g3-h1_g6-j1_h2-i1_j2-k1WURCSPDB2Glycan 1.1.0
[][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}}[(6+1)][a-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}[(6+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}}}}}LINUCSPDB-CARE
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 645 / 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: 2.67 Å3/Da / Density % sol: 53.97 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop
Details: 0.056 M Sodium phosphate monobasic monohydrate, 1.344 M Potassium phosphate dibasic, pH 8.2.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 10, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 49043 / % possible obs: 98.8 % / Redundancy: 4.7 % / CC1/2: 0.987 / CC star: 0.997 / Rpim(I) all: 0.109 / Rrim(I) all: 0.238 / Net I/σ(I): 18.2
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 3.7 % / Num. unique obs: 2458 / CC1/2: 0.636 / CC star: 0.882 / Rpim(I) all: 0.443 / Rrim(I) all: 0.886 / % possible all: 98.3

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
HKL-2000data scaling
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→28.87 Å / SU ML: 0.21 / Cross valid method: NONE / σ(F): 1.38 / Phase error: 22.8 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2219 2526 5.16 %
Rwork0.1888 --
obs0.1905 48955 96.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.9→28.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4016 0 276 645 4937
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_dihedral_angle_d12.2981637
X-RAY DIFFRACTIONf_chiral_restr0.057721
X-RAY DIFFRACTIONf_plane_restr0.005747
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.940.2871150.22392020X-RAY DIFFRACTION77
1.94-1.980.29981460.22382640X-RAY DIFFRACTION99
1.98-2.020.25411560.21522573X-RAY DIFFRACTION99
2.02-2.070.27441560.212641X-RAY DIFFRACTION99
2.07-2.120.26631500.20132599X-RAY DIFFRACTION98
2.12-2.170.23271640.19992613X-RAY DIFFRACTION99
2.18-2.240.23181540.19422624X-RAY DIFFRACTION99
2.24-2.310.25781340.19442632X-RAY DIFFRACTION99
2.31-2.390.26811240.19242611X-RAY DIFFRACTION98
2.39-2.490.23491420.18472608X-RAY DIFFRACTION98
2.49-2.60.21871270.18362481X-RAY DIFFRACTION93
2.6-2.740.21061480.17152629X-RAY DIFFRACTION99
2.74-2.910.21621330.17372647X-RAY DIFFRACTION100
2.91-3.140.21751390.17412688X-RAY DIFFRACTION100
3.14-3.450.18041370.16772658X-RAY DIFFRACTION99
3.45-3.950.16941440.16812626X-RAY DIFFRACTION98
3.95-4.970.21151270.16812494X-RAY DIFFRACTION92
4.97-28.870.23011300.23242645X-RAY DIFFRACTION96
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
17.8944-0.1498-5.34413.1241-1.484.4190.0375-0.66650.4450.72720.028-0.3807-0.36460.85790.00690.22580.0006-0.0590.1827-0.02120.214.645-14.47113.04
21.2936-0.0293-0.72141.93990.17692.4512-0.03050.18610.0296-0.14790.05660.00350.03440.06860.0070.1903-0.0103-0.00860.19690.01680.1646-1.698-10.304-2.817
36.1824-2.0835-0.50146.61621.19585.6718-0.0386-0.750.6080.55420.0846-0.0326-0.44260.46350.03110.2084-0.03750.01940.194-0.01350.17010.241-7.06311.092
41.7381-0.8747-0.5411.73851.00280.99980.03540.01250.1255-0.1726-0.00730.0205-0.03810.0987-0.05390.24530.01870.03480.18150.02490.164210.097-14.047-12.553
52.9499-1.3920.00345.67320.40152.95470.0633-0.23260.51830.0640.0596-0.3395-0.4116-0.0245-0.05320.18-0.01290.04010.1578-0.00190.2277.343-4.816-0.506
60.5782-0.4133-0.23032.07910.92070.41130.04310.02080.1306-0.0151-0.0497-0.0966-0.0022-0.0230.00480.2171-0.01660.02440.22040.00220.182916.388-20.539-8.234
73.01361.20830.55333.98231.84254.51340.0229-0.15750.0492-0.0615-0.2119-0.01210.0957-0.11950.15850.12250.03060.03010.12640.02640.145819.045-26.755-6.41
82.1081-0.348-0.39791.08790.01731.1436-0.0989-0.0929-0.06350.07520.07460.09150.00530.0510.03030.1741-0.00950.00430.1173-0.00720.1233.146-23.4647.946
94.0169-1.53181.59034.6512-2.45312.7035-0.0162-0.13940.30960.1340.0973-0.2746-0.19590.0207-0.06260.20880.00650.05590.17070.00150.2042-8.693-10.12611.669
106.2454-5.7178-5.30328.1116.68025.66110.55610.57440.2579-0.7193-0.3935-0.3504-0.6566-0.34-0.15560.26180.01150.02970.30540.04960.2647-5.206-3.137-7.222
112.2446-2.32850.13176.9536-1.26974.03670.09090.8753-0.4051-0.04030.01020.2702-0.007-0.504-0.05310.160.0237-0.00070.192-0.04920.067116.506-35.9838.479
120.63420.3015-0.93771.7348-0.78232.0663-0.03330.0445-0.04090.0338-0.0184-0.10470.12720.04390.08580.19860.0114-0.0050.1569-0.01020.151129.479-39.45333.993
137.5851-1.26530.3055.3072-0.8423.3352-0.02520.1572-0.7651-0.21810.02680.35510.5471-0.1208-0.00610.2775-0.0170.02720.1643-0.020.167923.737-47.37133.335
141.17520.8019-0.71991.97370.25331.16310.0058-0.01870.0464-0.1055-0.05040.11650.00240.07680.0890.16530.00090.0090.1261-0.01320.128132.116-24.59521.965
154.67153.9153-3.37854.0366-3.98815.4663-0.1522-0.2294-0.2136-1.0484-0.1469-0.22770.53510.10580.22650.27180.00020.00660.1993-0.0420.167228.622-36.73417.892
163.23750.36340.1513.9253-1.76810.91920.1701-0.28450.28190.12840.0469-0.1478-0.00730.1585-0.19750.299-0.00730.01880.2476-0.04510.189724.595-38.47326.852
173.09360.6077-2.42092.68-1.24664.01540.2011-0.26770.1166-0.0397-0.2033-0.3036-0.21310.3546-0.04270.1958-0.02550.01340.14990.01280.198234.813-18.9525.538
183.00143.0220.8967.19131.65422.38510.03330.1092-0.18940.02070.19780.14580.1829-0.1892-0.15780.17940.0226-0.03280.2258-0.00410.130521.171-28.37418.316
191.10480.1059-0.74981.5575-0.36681.93810.01420.0642-0.01770.13820.07610.1039-0.0671-0.0387-0.09460.18320.01090.01220.1369-0.0160.148916.732-26.6737.155
200.9245-0.04050.4931.7643-0.75430.9459-0.0447-0.034-0.13880.14360.03580.04190.08860.02330.00090.2688-0.01150.05010.1524-0.00870.144419.814-38.8146.973
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 44:49 )A44 - 49
2X-RAY DIFFRACTION2( CHAIN A AND RESID 50:65 )A50 - 65
3X-RAY DIFFRACTION3( CHAIN A AND RESID 66:75 )A66 - 75
4X-RAY DIFFRACTION4( CHAIN A AND RESID 76:105 )A76 - 105
5X-RAY DIFFRACTION5( CHAIN A AND RESID 106:123 )A106 - 123
6X-RAY DIFFRACTION6( CHAIN A AND RESID 124:166 )A124 - 166
7X-RAY DIFFRACTION7( CHAIN A AND RESID 167:193 )A167 - 193
8X-RAY DIFFRACTION8( CHAIN A AND RESID 194:277 )A194 - 277
9X-RAY DIFFRACTION9( CHAIN A AND RESID 278:299 )A278 - 299
10X-RAY DIFFRACTION10( CHAIN A AND RESID 300:306 )A300 - 306
11X-RAY DIFFRACTION11( CHAIN B AND RESID 44:52 )B44 - 52
12X-RAY DIFFRACTION12( CHAIN B AND RESID 53:105 )B53 - 105
13X-RAY DIFFRACTION13( CHAIN B AND RESID 106:121 )B106 - 121
14X-RAY DIFFRACTION14( CHAIN B AND RESID 122:140 )B122 - 140
15X-RAY DIFFRACTION15( CHAIN B AND RESID 141:153 )B141 - 153
16X-RAY DIFFRACTION16( CHAIN B AND RESID 154:161 )B154 - 161
17X-RAY DIFFRACTION17( CHAIN B AND RESID 162:177 )B162 - 177
18X-RAY DIFFRACTION18( CHAIN B AND RESID 178:192 )B178 - 192
19X-RAY DIFFRACTION19( CHAIN B AND RESID 193:260 )B193 - 260
20X-RAY DIFFRACTION20( CHAIN B AND RESID 261:306 )B261 - 306

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