[English] 日本語
Yorodumi
- PDB-6t2o: Prominent members of the human gut microbiota express endo-acting... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6t2o
TitleProminent members of the human gut microbiota express endo-acting O-glycanases to initiate mucin breakdown
ComponentsGlycosyl hydrolase family 16
KeywordsHYDROLASE / Human gut microbiota / mucin degradation / O-glycanases / GH16 / endo beta-galactosidase
Function / homologyGlycosyl hydrolases family 16 / Glycoside hydrolase family 16 / Glycosyl hydrolases family 16 (GH16) domain profile. / hydrolase activity, hydrolyzing O-glycosyl compounds / Concanavalin A-like lectin/glucanase domain superfamily / carbohydrate metabolic process / Glycosyl hydrolase family 16
Function and homology information
Biological speciesBacteroides caccae ATCC 43185 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsCrouch, L.I. / Liberato, M.V. / Ubranowicz, P.A. / Basle, A. / Lamb, C.A. / Cooke, K. / Doona, M. / Needham, S. / Brady, R.R. / Berrington, J.E. ...Crouch, L.I. / Liberato, M.V. / Ubranowicz, P.A. / Basle, A. / Lamb, C.A. / Cooke, K. / Doona, M. / Needham, S. / Brady, R.R. / Berrington, J.E. / Madubic, K. / Chater, P. / Zhang, F. / Linhardt, R.J. / Spence, D.I.R. / Bolam, D.N.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research CouncilBB/M029018/1 United Kingdom
CitationJournal: Nat Commun / Year: 2020
Title: Prominent members of the human gut microbiota express endo-acting O-glycanases to initiate mucin breakdown.
Authors: Crouch, L.I. / Liberato, M.V. / Urbanowicz, P.A. / Basle, A. / Lamb, C.A. / Stewart, C.J. / Cooke, K. / Doona, M. / Needham, S. / Brady, R.R. / Berrington, J.E. / Madunic, K. / Wuhrer, M. / ...Authors: Crouch, L.I. / Liberato, M.V. / Urbanowicz, P.A. / Basle, A. / Lamb, C.A. / Stewart, C.J. / Cooke, K. / Doona, M. / Needham, S. / Brady, R.R. / Berrington, J.E. / Madunic, K. / Wuhrer, M. / Chater, P. / Pearson, J.P. / Glowacki, R. / Martens, E.C. / Zhang, F. / Linhardt, R.J. / Spencer, D.I.R. / Bolam, D.N.
History
DepositionOct 9, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 8, 2020Provider: repository / Type: Initial release
Revision 1.1Aug 26, 2020Group: Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / pdbx_struct_conn_angle / struct_conn
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry
Revision 1.2Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
AAA: Glycosyl hydrolase family 16
BBB: Glycosyl hydrolase family 16
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,8298
Polymers64,5002
Non-polymers3286
Water2,414134
1
AAA: Glycosyl hydrolase family 16
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,4144
Polymers32,2501
Non-polymers1643
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
BBB: Glycosyl hydrolase family 16
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,4144
Polymers32,2501
Non-polymers1643
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)82.646, 82.646, 121.489
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number76
Space group name H-MP41

-
Components

#1: Protein Glycosyl hydrolase family 16


Mass: 32250.236 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides caccae ATCC 43185 (bacteria)
Gene: BACCAC_02680 / Production host: Escherichia coli (E. coli) / References: UniProt: A5ZIF0
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 134 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.22 Å3/Da / Density % sol: 61.76 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: 200 mM sodium malonate pH 7.0, 20% PEG 3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9159 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 21, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9159 Å / Relative weight: 1
ReflectionResolution: 2.05→82.65 Å / Num. obs: 51105 / % possible obs: 100 % / Redundancy: 7.4 % / CC1/2: 0.986 / Net I/σ(I): 6.3
Reflection shellResolution: 2.05→2.16 Å / Mean I/σ(I) obs: 1.6 / Num. unique obs: 3974 / CC1/2: 0.958

-
Processing

Software
NameVersionClassification
REFMAC5.8.0257refinement
xia2data reduction
DIALSdata reduction
PHASERphasing
Cootmodel building
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ILN

3iln


Resolution: 2.05→82.646 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.919 / SU B: 8.687 / SU ML: 0.114 / Cross valid method: FREE R-VALUE / ESU R: 0.148 / ESU R Free: 0.145
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2402 2613 5.12 %
Rwork0.1994 --
all0.202 --
obs-51036 99.941 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 41.008 Å2
Baniso -1Baniso -2Baniso -3
1--0.382 Å20 Å20 Å2
2---0.382 Å20 Å2
3---0.765 Å2
Refinement stepCycle: LAST / Resolution: 2.05→82.646 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3919 0 18 134 4071
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0134045
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173626
X-RAY DIFFRACTIONr_angle_refined_deg1.5251.6425480
X-RAY DIFFRACTIONr_angle_other_deg1.2581.588431
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.585481
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.3723.756221
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.17715668
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.0391516
X-RAY DIFFRACTIONr_chiral_restr0.0670.2487
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024531
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02881
X-RAY DIFFRACTIONr_nbd_refined0.1880.2662
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1760.23349
X-RAY DIFFRACTIONr_nbtor_refined0.170.21871
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0770.21945
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1370.2171
X-RAY DIFFRACTIONr_metal_ion_refined0.0780.27
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2650.213
X-RAY DIFFRACTIONr_nbd_other0.1890.240
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.5910.26
X-RAY DIFFRACTIONr_mcbond_it1.2042.8321930
X-RAY DIFFRACTIONr_mcbond_other1.2042.8321929
X-RAY DIFFRACTIONr_mcangle_it1.7794.2412409
X-RAY DIFFRACTIONr_mcangle_other1.7784.2422410
X-RAY DIFFRACTIONr_scbond_it1.58732115
X-RAY DIFFRACTIONr_scbond_other1.58632116
X-RAY DIFFRACTIONr_scangle_it2.4544.4223071
X-RAY DIFFRACTIONr_scangle_other2.4544.4223072
X-RAY DIFFRACTIONr_lrange_it4.19131.6334421
X-RAY DIFFRACTIONr_lrange_other4.17531.5374407
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
2.05-2.1030.3021870.29335930.29437870.8130.78899.81520.287
2.103-2.1610.2771800.25434800.25536620.8560.86899.94540.246
2.161-2.2240.2671700.24133630.24235350.8790.88799.94340.228
2.224-2.2920.2761990.2732780.2734920.8830.87899.57040.257
2.292-2.3670.2841700.21931920.22233620.8980.9171000.206
2.367-2.450.2831710.21630640.21932360.8980.92399.96910.203
2.45-2.5420.2941380.22129990.22431380.8870.9299.96810.209
2.542-2.6460.2811780.21528410.21930190.9040.9251000.207
2.646-2.7640.2311530.21427650.21529190.9160.92299.96570.208
2.764-2.8980.2541560.21325950.21627510.9240.9311000.212
2.898-3.0550.251360.21825060.21926420.9090.9211000.222
3.055-3.240.2871270.2223610.22324880.8910.921000.228
3.24-3.4630.2251110.21122480.21223590.9410.941000.224
3.463-3.740.221060.20520850.20621910.9480.9511000.222
3.74-4.0960.2091060.1819010.18220070.9520.961000.203
4.096-4.5790.197950.14117340.14418290.9610.971000.172
4.579-5.2840.198690.14515410.14716100.9620.9761000.173
5.284-6.4650.228610.17513070.17713680.9620.9661000.203
6.465-9.1150.194660.1710000.17110660.9560.9641000.193
9.115-82.6460.299340.2295690.2346040.9630.95599.83440.254
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)
11.38430.59870.0813.43380.54682.0476-0.02970.09840.0455-0.0104-0.04840.1366-0.0705-0.19370.07820.08320.03990.02010.04280.00470.014-35.038-21.15330.3163
23.1189-0.0410.34921.4163-0.08912.5605-0.0036-0.22240.02030.0167-0.0051-0.0812-0.12230.10550.00860.016-0.0052-0.02290.0823-0.01070.0536-17.0618-22.067630.9439
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLAAA34 - 274
2X-RAY DIFFRACTION2ALLBBB33 - 401

+
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://pdbjlvh1.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