[English] 日本語
Yorodumi
- PDB-8u48: Crystal structure of Bacteroides thetaiotamicron BT1285 D161A-E16... -

+
Open data


ID or keywords:

Loading...

-
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 (GH18) domain profile. / Glycosyl hydrolases family 18 / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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.

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more