[English] 日本語
Yorodumi
- PDB-5jow: Bacteroides ovatus Xyloglucan PUL GH43A -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5jow
TitleBacteroides ovatus Xyloglucan PUL GH43A
ComponentsNon-reducing end alpha-L-arabinofuranosidase BoGH43A
KeywordsHYDROLASE / Glycoside hydrolase / GH43
Function / homology
Function and homology information


symbiotic process benefiting host / xyloglucan catabolic process / non-reducing end alpha-L-arabinofuranosidase / alpha-L-arabinofuranosidase activity / periplasmic space
Similarity search - Function
Beta-xylosidase, C-terminal Concanavalin A-like domain / Beta xylosidase C-terminal Concanavalin A-like domain / Glycoside hydrolase, family 43 / Glycosyl hydrolases family 43 / Glycosyl hydrolase domain; family 43 / 5 Propeller / Tachylectin-2; Chain A / Glycosyl hydrolase, five-bladed beta-propellor domain superfamily / Jelly Rolls - #200 / Concanavalin A-like lectin/glucanase domain superfamily ...Beta-xylosidase, C-terminal Concanavalin A-like domain / Beta xylosidase C-terminal Concanavalin A-like domain / Glycoside hydrolase, family 43 / Glycosyl hydrolases family 43 / Glycosyl hydrolase domain; family 43 / 5 Propeller / Tachylectin-2; Chain A / Glycosyl hydrolase, five-bladed beta-propellor domain superfamily / Jelly Rolls - #200 / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Non-reducing end alpha-L-arabinofuranosidase BoGH43A
Similarity search - Component
Biological speciesBacteroides ovatus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsThompson, A.J. / Hemsworth, G.R. / Stepper, J. / Sobala, L.F. / Coyle, T. / Larsbrink, J. / Spadiut, O. / Stubbs, K.A. / Brumer, H. / Davies, G.J.
Funding support United Kingdom, 3items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research CouncilBB/K00591X/1 United Kingdom
Biotechnology and Biological Sciences Research CouncilBB/I014802/1 United Kingdom
European Research Council322942 United Kingdom
CitationJournal: Open Biology / Year: 2016
Title: Structural dissection of a complex Bacteroides ovatus gene locus conferring xyloglucan metabolism in the human gut.
Authors: Hemsworth, G.R. / Thompson, A.J. / Stepper, J. / Sobala, F. / Coyle, T. / Larsbrink, J. / Spadiut, O. / Goddard-Borger, E.D. / Stubbs, K.A. / Brumer, H. / Davies, G.J.
History
DepositionMay 3, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Aug 10, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 30, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Non-reducing end alpha-L-arabinofuranosidase BoGH43A
B: Non-reducing end alpha-L-arabinofuranosidase BoGH43A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,74827
Polymers116,0762
Non-polymers1,67225
Water23,6901315
1
A: Non-reducing end alpha-L-arabinofuranosidase BoGH43A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,78112
Polymers58,0381
Non-polymers74311
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Non-reducing end alpha-L-arabinofuranosidase BoGH43A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,96715
Polymers58,0381
Non-polymers92914
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)75.432, 91.172, 156.856
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21221
Components on special symmetry positions
IDModelComponents
11B-177-

LYS

-
Components

#1: Protein Non-reducing end alpha-L-arabinofuranosidase BoGH43A / Glycosyl hydrolase family protein 43A / BoGH43A


Mass: 58037.914 Da / Num. of mol.: 2 / Fragment: UNP residues 21-526
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides ovatus (bacteria) / Gene: BACOVA_02654 / Plasmid: pET-YSBLLIC / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): TUNER
References: UniProt: A7LXT8, non-reducing end alpha-L-arabinofuranosidase
#2: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#3: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 23 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1315 / 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: 2.32 Å3/Da / Density % sol: 47.06 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: 0.1 M Tris pH 7.2 - 7.8, 0.18 M magnesium chloride and 12% (w/v) PEG-6000

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Aug 14, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 1.6→46.69 Å / Num. obs: 142867 / % possible obs: 100 % / Redundancy: 8.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.092 / Net I/σ(I): 14.5
Reflection shellResolution: 1.6→1.63 Å / Redundancy: 8 % / Rmerge(I) obs: 1.05 / Mean I/σ(I) obs: 1.9 / % possible all: 100

-
Processing

Software
NameVersionClassification
REFMAC5.8.0123refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: GH43B to be deposited

Resolution: 1.6→46.69 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.966 / SU B: 2.889 / SU ML: 0.05 / Cross valid method: THROUGHOUT / ESU R: 0.083 / ESU R Free: 0.072 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.16698 7115 5 %RANDOM
Rwork0.12528 ---
obs0.12735 135666 99.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 20.095 Å2
Baniso -1Baniso -2Baniso -3
1--0.2 Å20 Å20 Å2
2--0.5 Å20 Å2
3----0.3 Å2
Refinement stepCycle: 1 / Resolution: 1.6→46.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7898 0 108 1315 9321
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0198493
X-RAY DIFFRACTIONr_bond_other_d0.0020.027770
X-RAY DIFFRACTIONr_angle_refined_deg1.3651.94711578
X-RAY DIFFRACTIONr_angle_other_deg0.927317946
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7751090
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.1823.737396
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.906151309
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.2591545
X-RAY DIFFRACTIONr_chiral_restr0.0910.21220
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0219712
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022029
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.5310.4354118
X-RAY DIFFRACTIONr_mcbond_other1.5310.444115
X-RAY DIFFRACTIONr_mcangle_it2.0375163
X-RAY DIFFRACTIONr_mcangle_other2.0375164
X-RAY DIFFRACTIONr_scbond_it1.9714373
X-RAY DIFFRACTIONr_scbond_other1.9714373
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.376371
X-RAY DIFFRACTIONr_long_range_B_refined4.31510420
X-RAY DIFFRACTIONr_long_range_B_other4.31510421
X-RAY DIFFRACTIONr_rigid_bond_restr1.53838207
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded8.78857933
LS refinement shellResolution: 1.6→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.253 514 -
Rwork0.199 9935 -
obs--99.99 %

+
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