[English] 日本語
Yorodumi
- PDB-5ta9: Crystal structure of BuGH117Bwt in complex with neoagarobiose -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5ta9
TitleCrystal structure of BuGH117Bwt in complex with neoagarobiose
ComponentsGlycoside Hydrolase
KeywordsHYDROLASE / agarase / glycoside hydrolase
Function / homology
Function and homology information


hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate metabolic process
Similarity search - Function
: / 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 / Mainly Beta
Similarity search - Domain/homology
3,6-anhydro-alpha-L-galactopyranose / beta-D-galactopyranose / Glycoside Hydrolase
Similarity search - Component
Biological speciesBacteroides uniformis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.4 Å
AuthorsPluvinage, B. / Boraston, A.B.
CitationJournal: Nat Commun / Year: 2018
Title: Molecular basis of an agarose metabolic pathway acquired by a human intestinal symbiont.
Authors: Pluvinage, B. / Grondin, J.M. / Amundsen, C. / Klassen, L. / Moote, P.E. / Xiao, Y. / Thomas, D. / Pudlo, N.A. / Anele, A. / Martens, E.C. / Inglis, G.D. / Uwiera, R.E.R. / Boraston, A.B. / Abbott, D.W.
History
DepositionSep 9, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 13, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _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.ptnr2_auth_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Mar 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Glycoside Hydrolase
B: Glycoside Hydrolase
C: Glycoside Hydrolase
D: Glycoside Hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)184,01416
Polymers182,5484
Non-polymers1,46612
Water8,053447
1
A: Glycoside Hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,0044
Polymers45,6371
Non-polymers3673
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Glycoside Hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,0044
Polymers45,6371
Non-polymers3673
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Glycoside Hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,0044
Polymers45,6371
Non-polymers3673
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Glycoside Hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,0044
Polymers45,6371
Non-polymers3673
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
A: Glycoside Hydrolase
B: Glycoside Hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,0078
Polymers91,2742
Non-polymers7336
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8720 Å2
ΔGint-32 kcal/mol
Surface area27110 Å2
MethodPISA
6
C: Glycoside Hydrolase
D: Glycoside Hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,0078
Polymers91,2742
Non-polymers7336
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8670 Å2
ΔGint-30 kcal/mol
Surface area26680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.511, 104.380, 198.500
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein
Glycoside Hydrolase


Mass: 45636.973 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides uniformis (bacteria) / Strain: NP1 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0A2D0TCD6*PLUS
#2: Sugar
ChemComp-GAL / beta-D-galactopyranose / beta-D-galactose / D-galactose / galactose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGalpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-galactopyranoseCOMMON NAMEGMML 1.0
b-D-GalpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GalSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Sugar
ChemComp-AAL / 3,6-anhydro-alpha-L-galactopyranose / 3,6-ANHYDRO-L-GALACTOSE / 3,6-anhydro-alpha-L-galactose / 3,6-anhydro-galactose


Type: L-saccharide, alpha linking / Mass: 162.141 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C6H10O5
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 447 / 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: 2.37 Å3/Da / Density % sol: 48.09 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 0.1-0.18M LiSo4, 0.1M Tris-HCl, 25-30% PEG 4000

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97949 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Jul 4, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.4→99.25 Å / Num. obs: 65697 / % possible obs: 96 % / Redundancy: 8.3 % / CC1/2: 0.989 / Rmerge(I) obs: 0.16 / Net I/σ(I): 8.2
Reflection shellResolution: 2.4→2.53 Å / Redundancy: 8.6 % / Rmerge(I) obs: 0.54 / Mean I/σ(I) obs: 3.6 / CC1/2: 0.825 / % possible all: 90

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
REFMAC5.8.0155refinement
PDB_EXTRACT3.2data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→99.25 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.907 / SU B: 10.431 / SU ML: 0.231 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.5 / ESU R Free: 0.279
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2531 3303 5 %RANDOM
Rwork0.2071 ---
obs0.2095 62315 95.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 95.2 Å2 / Biso mean: 41.588 Å2 / Biso min: 11.89 Å2
Baniso -1Baniso -2Baniso -3
1--0.32 Å20 Å20 Å2
2---2 Å20 Å2
3---2.32 Å2
Refinement stepCycle: final / Resolution: 2.4→99.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11798 0 96 447 12341
Biso mean--45.37 32.04 -
Num. residues----1476
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0212247
X-RAY DIFFRACTIONr_bond_other_d0.0020.0210915
X-RAY DIFFRACTIONr_angle_refined_deg1.3041.93716640
X-RAY DIFFRACTIONr_angle_other_deg0.892325247
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0951472
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.55924.148581
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.95151933
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.8361560
X-RAY DIFFRACTIONr_chiral_restr0.0750.21688
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02113806
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022854
X-RAY DIFFRACTIONr_mcbond_it1.724.2095900
X-RAY DIFFRACTIONr_mcbond_other1.7194.2095899
X-RAY DIFFRACTIONr_mcangle_it2.8376.3077368
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.344 252 -
Rwork0.284 4219 -
all-4471 -
obs--89.15 %

+
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