[English] 日本語
Yorodumi
- PDB-6e57: Bacteroides ovatus mixed-linkage glucan utilization locus (MLGUL)... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6.0E+57
TitleBacteroides ovatus mixed-linkage glucan utilization locus (MLGUL) SGBP-B in complex with mixed-linkage heptasaccharide
Componentssurface glycan binding protein B
KeywordsSUGAR BINDING PROTEIN / mixed-linkage beta-glucan / surface glycan binding protein / Bacteroides
Function / homologyImmunoglobulin-like fold / beta-cellopentaose / PHOSPHATE ION / PKD domain-containing protein
Function and homology information
Biological speciesBacteroides ovatus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.71 Å
AuthorsKoropatkin, N.M. / Schnizlein, M. / Bahr, C.M.E.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM118475 United States
CitationJournal: Cell.Mol.Life Sci. / Year: 2019
Title: Surface glycan-binding proteins are essential for cereal beta-glucan utilization by the human gut symbiont Bacteroides ovatus.
Authors: Tamura, K. / Foley, M.H. / Gardill, B.R. / Dejean, G. / Schnizlein, M. / Bahr, C.M.E. / Louise Creagh, A. / van Petegem, F. / Koropatkin, N.M. / Brumer, H.
History
DepositionJul 19, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 29, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2019Group: Data collection / Database references / Category: chem_comp / citation / citation_author
Item: _chem_comp.type / _citation.journal_volume ..._chem_comp.type / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / struct_asym / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Mar 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: surface glycan binding protein B
B: surface glycan binding protein B
C: surface glycan binding protein B
D: surface glycan binding protein B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)186,88528
Polymers182,7134
Non-polymers4,17224
Water2,522140
1
A: surface glycan binding protein B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,0349
Polymers45,6781
Non-polymers1,3568
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: surface glycan binding protein B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,0255
Polymers45,6781
Non-polymers3474
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: surface glycan binding protein B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,9728
Polymers45,6781
Non-polymers1,2947
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: surface glycan binding protein B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,8546
Polymers45,6781
Non-polymers1,1765
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)156.438, 243.652, 76.059
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

-
Protein / Sugars , 2 types, 7 molecules ABCD

#1: Protein
surface glycan binding protein B


Mass: 45678.328 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides ovatus (strain ATCC 8483 / DSM 1896 / JCM 5824 / NCTC 11153) (bacteria)
Strain: ATCC 8483 / DSM 1896 / JCM 5824 / NCTC 11153 / Gene: BACOVA_02744 / Production host: Escherichia coli (E. coli) / References: UniProt: A7LY28
#2: Polysaccharide beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D- ...beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose / beta-cellopentaose


Type: oligosaccharide, Oligosaccharide / Class: Metabolism / Mass: 828.719 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: beta-cellopentaose
DescriptorTypeProgram
DGlcpb1-4DGlcpb1-4DGlcpb1-4DGlcpb1-4DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,5,4/[a2122h-1b_1-5]/1-1-1-1-1/a4-b1_b4-c1_c4-d1_d4-e1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(4+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{}}}}}LINUCSPDB-CARE

-
Non-polymers , 4 types, 161 molecules

#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: PO4
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 140 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.97 Å3/Da / Density % sol: 68.99 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: JCSG Plus screen in C5 (0.8 M NaH2PO4, 0.8 M KH2PO4, 0.1M sodium HEPES pH 7.5)
Temp details: room

-
Data collection

DiffractionMean temperature: 100 K / Ambient temp details: cryogenic
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.9786 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 8, 2016
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 2.71→78.34 Å / Num. obs: 78048 / % possible obs: 97.74 % / Redundancy: 5.7 % / Rmerge(I) obs: 0.1238 / Net I/σ(I): 10.44
Reflection shellResolution: 2.71→2.807 Å / Rmerge(I) obs: 0.8111 / Mean I/σ(I) obs: 2.42 / Num. unique obs: 7714 / CC1/2: 0.7 / % possible all: 98.32

-
Processing

Software
NameVersionClassification
REFMAC5.8.0222refinement
xia2data scaling
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 2.71→78.34 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.913 / SU B: 25.517 / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.27
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2382 3927 5 %RANDOM
Rwork0.1943 ---
obs0.1965 74118 97.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 131.11 Å2 / Biso mean: 56.498 Å2 / Biso min: 24.38 Å2
Baniso -1Baniso -2Baniso -3
1--0.41 Å20 Å20 Å2
2--0.3 Å20 Å2
3---0.12 Å2
Refinement stepCycle: final / Resolution: 2.71→78.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11933 0 260 140 12333
Biso mean--74.86 43.78 -
Num. residues----1562
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.01412401
X-RAY DIFFRACTIONr_bond_other_d0.0010.01710928
X-RAY DIFFRACTIONr_angle_refined_deg0.8611.68716937
X-RAY DIFFRACTIONr_angle_other_deg0.6981.6625572
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8351557
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.00224.93570
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.351151964
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.0041536
X-RAY DIFFRACTIONr_chiral_restr0.0390.21794
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.0213711
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022157
X-RAY DIFFRACTIONr_rigid_bond_restr0.576323329
X-RAY DIFFRACTIONr_sphericity_free44.2865103
X-RAY DIFFRACTIONr_sphericity_bonded24.727523158
LS refinement shellResolution: 2.71→2.78 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.342 303 -
Rwork0.322 5389 -
all-5692 -
obs--98.79 %
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)
10.7180.5414-0.44081.0344-0.39670.44580.027-0.1561-0.16750.0715-0.00530.08730.13220.1129-0.02170.150.0291-0.08220.06070.05930.1695-37.009731.5674-13.9335
20.8531-0.2527-0.67870.41140.73611.9040.07650.3672-0.2157-0.12980.0338-0.05220.0082-0.0896-0.11030.2068-0.0979-0.0920.321-0.04930.189-0.812447.61131.4166
32.97970.89610.26590.4520.06730.2218-0.0078-0.0682-0.53070.02770.0735-0.27710.16360.025-0.06570.2399-0.0177-0.10540.0958-0.00880.21389.700734.996117.9525
42.8201-0.907-0.71150.44550.11850.578-0.05020.3007-0.4567-0.1119-0.03530.21910.1205-0.09740.08550.1746-0.0468-0.080.0739-0.06650.2001-49.782229.3961-32.1477
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A22 - 420
2X-RAY DIFFRACTION2B33 - 420
3X-RAY DIFFRACTION3C32 - 505
4X-RAY DIFFRACTION4D33 - 420

+
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