[English] 日本語
Yorodumi
- PDB-5joz: Bacteroides ovatus Xyloglucan PUL GH43B -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5joz
TitleBacteroides ovatus Xyloglucan PUL GH43B
ComponentsNon-reducing end alpha-L-arabinofuranosidase BoGH43B
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 BoGH43B
Similarity search - Component
Biological speciesBacteroides ovatus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.28 Å
AuthorsHemsworth, G.R. / Thompson, A.J. / 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
Revision 1.2Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Non-reducing end alpha-L-arabinofuranosidase BoGH43B
B: Non-reducing end alpha-L-arabinofuranosidase BoGH43B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,6904
Polymers114,6102
Non-polymers802
Water3,765209
1
A: Non-reducing end alpha-L-arabinofuranosidase BoGH43B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,3452
Polymers57,3051
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Non-reducing end alpha-L-arabinofuranosidase BoGH43B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,3452
Polymers57,3051
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)91.460, 71.400, 160.300
Angle α, β, γ (deg.)90.00, 94.78, 90.00
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein Non-reducing end alpha-L-arabinofuranosidase BoGH43B / Glycosyl hydrolase family protein 43B / BoGH43B


Mass: 57305.031 Da / Num. of mol.: 2 / Fragment: UNP residues 24-529
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides ovatus (bacteria) / Gene: BACOVA_02656 / Plasmid: pET-21a / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A7LXU0, non-reducing end alpha-L-arabinofuranosidase
#2: Chemical ChemComp-CA / CALCIUM ION


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


Mass: 18.015 Da / Num. of mol.: 209 / 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: 2.28 Å3/Da / Density % sol: 45.94 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 5 / Details: 0.2 M sodium acetate pH 5, 20-30% PEG-3350

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 17, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.28→52.19 Å / Num. obs: 46976 / % possible obs: 99.6 % / Redundancy: 4.1 % / Rmerge(I) obs: 0.092 / Net I/σ(I): 11.1
Reflection shellResolution: 2.28→2.34 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.624 / Mean I/σ(I) obs: 2.3 / % possible all: 99.5

-
Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1yrz

1yrz


Resolution: 2.28→52.19 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.906 / SU B: 8.557 / SU ML: 0.202 / Cross valid method: THROUGHOUT / ESU R: 0.35 / ESU R Free: 0.245 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25023 2358 5 %RANDOM
Rwork0.19222 ---
obs0.19513 44617 99.54 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 34.601 Å2
Baniso -1Baniso -2Baniso -3
1-1.38 Å20 Å20.83 Å2
2---3.41 Å20 Å2
3---1.87 Å2
Refinement stepCycle: 1 / Resolution: 2.28→52.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7723 0 2 209 7934
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0197963
X-RAY DIFFRACTIONr_bond_other_d0.0020.027101
X-RAY DIFFRACTIONr_angle_refined_deg1.3241.9310884
X-RAY DIFFRACTIONr_angle_other_deg0.911316311
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7751009
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.90523.711353
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.198151098
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.6511538
X-RAY DIFFRACTIONr_chiral_restr0.0770.21167
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0219217
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021925
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_it3.1713.4254042
X-RAY DIFFRACTIONr_mcbond_other3.1683.4244041
X-RAY DIFFRACTIONr_mcangle_it4.4745.135049
X-RAY DIFFRACTIONr_mcangle_other4.4735.135050
X-RAY DIFFRACTIONr_scbond_it3.5933.6183921
X-RAY DIFFRACTIONr_scbond_other3.5923.6183922
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.0665.3165835
X-RAY DIFFRACTIONr_long_range_B_refined6.6227.3198462
X-RAY DIFFRACTIONr_long_range_B_other6.62127.3158433
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.28→2.339 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.339 164 -
Rwork0.276 3270 -
obs--99.51 %

+
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