[English] 日本語
Yorodumi
- PDB-6gpa: Beta-1,4-galactanase from Bacteroides thetaiotaomicron with galactose -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6gpa
TitleBeta-1,4-galactanase from Bacteroides thetaiotaomicron with galactose
ComponentsArabinogalactan endo-beta-1,4-galactanase
KeywordsCARBOHYDRATE / Glycosyl hydrolase / Galactosidase / Endo-galactanase / galactose
Function / homologyarabinogalactan endo-beta-1,4-galactanase / arabinogalactan endo-1,4-beta-galactosidase activity / Glycosyl hydrolase family 53 / Glycosyl hydrolase family 53 / glucosidase activity / pectin catabolic process / Glycoside hydrolase superfamily / beta-D-galactopyranose / Arabinogalactan endo-beta-1,4-galactanase
Function and homology information
Biological speciesBacteroides thetaiotaomicron (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.79 Å
AuthorsHekelaar, J. / Boger, M. / Leeuwen van, S.S. / Lammerts van Bueren, A. / Dijkhuizen, L.
Funding support Netherlands, 1items
OrganizationGrant numberCountry
Netherlands Organisation for Scientific Research Netherlands
CitationJournal: J. Struct. Biol. / Year: 2019
Title: Structural and functional characterization of a family GH53 beta-1,4-galactanase from Bacteroides thetaiotaomicron that facilitates degradation of prebiotic galactooligosaccharides.
Authors: Boger, M. / Hekelaar, J. / van Leeuwen, S.S. / Dijkhuizen, L. / Lammerts van Bueren, A.
History
DepositionJun 5, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 26, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 6, 2019Group: Data collection / Database references / Category: citation / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _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 / 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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: Arabinogalactan endo-beta-1,4-galactanase
B: Arabinogalactan endo-beta-1,4-galactanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,2174
Polymers70,8562
Non-polymers3602
Water13,007722
1
A: Arabinogalactan endo-beta-1,4-galactanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,6082
Polymers35,4281
Non-polymers1801
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Arabinogalactan endo-beta-1,4-galactanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,6082
Polymers35,4281
Non-polymers1801
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)47.544, 45.632, 138.760
Angle α, β, γ (deg.)90.000, 99.800, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Arabinogalactan endo-beta-1,4-galactanase


Mass: 35428.172 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Sample sequence starts at -1
Source: (gene. exp.) Bacteroides thetaiotaomicron (strain ATCC 29148 / DSM 2079 / NCTC 10582 / E50 / VPI-5482) (bacteria)
Strain: ATCC 29148 / DSM 2079 / NCTC 10582 / E50 / VPI-5482 / Gene: BT_4668 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q89YR3, arabinogalactan endo-beta-1,4-galactanase
#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.: 2
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 722 / 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: 2.09 Å3/Da / Density % sol: 41.24 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 20-23% PEG6000, 200 mM NH4Cl, MES pH 6.0

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.9762 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 1, 2015 / Details: KB-mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 1.79→46.85 Å / Num. obs: 53053 / % possible obs: 96.1 % / Redundancy: 2.6 % / CC1/2: 0.974 / Rmerge(I) obs: 0.11 / Rpim(I) all: 0.085 / Rrim(I) all: 0.14 / Net I/σ(I): 8.6 / Num. measured all: 138347 / Scaling rejects: 92
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.79-1.832.40.40326870.5140.3280.52280.5
8.96-46.852.70.0514420.990.0390.06593.2

-
Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation1.79 Å46.85 Å
Translation1.79 Å46.85 Å

-
Processing

Software
NameVersionClassificationNB
REFMAC5.8.0222refinement
XDSdata reduction
Aimless0.3.11data scaling
PHASER2.5.6phasing
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6GP5

6gp5


Resolution: 1.79→46.84 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.906 / SU B: 3.649 / SU ML: 0.112 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.143 / ESU R Free: 0.137
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.22 2600 4.9 %RANDOM
Rwork0.1703 ---
obs0.1728 50408 95.47 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 49.15 Å2 / Biso mean: 10.166 Å2 / Biso min: 1.04 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å2-0 Å2
2---0.02 Å2-0 Å2
3---0.01 Å2
Refinement stepCycle: final / Resolution: 1.79→46.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4930 0 24 722 5676
Biso mean--21.21 21.28 -
Num. residues----624
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0145074
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174477
X-RAY DIFFRACTIONr_angle_refined_deg1.4571.6546885
X-RAY DIFFRACTIONr_angle_other_deg0.9871.64810500
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3735622
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.51424.566265
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.76715852
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.1751518
X-RAY DIFFRACTIONr_chiral_restr0.0750.2640
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.025708
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02936
LS refinement shellResolution: 1.793→1.84 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.257 182 -
Rwork0.23 3189 -
all-3371 -
obs--82.7 %

+
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