[English] 日本語
Yorodumi
- PDB-7dt1: The structure of Lactobacillus fermentum 4,6-alpha-Glucanotransferase -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7dt1
TitleThe structure of Lactobacillus fermentum 4,6-alpha-Glucanotransferase
ComponentsDextransucrase
KeywordsTRANSFERASE / Glycoside Hydrolase Family 70 / U-course / 4 / 6-alpha-Glucanotransferase
Function / homology
Function and homology information


dextransucrase activity / dextransucrase / glucan biosynthetic process / glucosyltransferase activity / metal ion binding
Similarity search - Function
Glycoside hydrolase, family 70, catalytic domain / Glycosyl hydrolase family 70 / Glycoside hydrolase superfamily
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / dextransucrase
Similarity search - Component
Biological speciesLimosilactobacillus fermentum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4300227139 Å
AuthorsYang, W.K. / Yong, Y.H. / Wu, L. / Chen, S. / Zhou, J.H. / Wu, J.
CitationJournal: Food Biosci / Year: 2022
Title: Characterization of a new 4,6-alpha-glucanotransferase from Limosilactobacillus fermentum NCC 3057 with ability of synthesizing low molecular mass isomalto-/maltopolysaccharide
Authors: Yang, W. / Sheng, L. / Chen, S. / Wang, L. / Su, L. / Wu, J.
History
DepositionJan 4, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 12, 2022Provider: repository / Type: Initial release
Revision 1.1Aug 10, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / pdbx_initial_refinement_model
Item: _citation.country

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Dextransucrase
B: Dextransucrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)239,04465
Polymers234,8872
Non-polymers4,15763
Water20,8251156
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10630 Å2
ΔGint-3 kcal/mol
Surface area63240 Å2
Unit cell
Length a, b, c (Å)99.830, 106.080, 106.020
Angle α, β, γ (deg.)90.000, 104.832, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein Dextransucrase / Sucrose 6-glucosyltransferase


Mass: 117443.430 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Limosilactobacillus fermentum (bacteria)
Production host: Escherichia coli K-12 (bacteria) / Strain (production host): K-12 / References: UniProt: A0A1Z2RUD1, dextransucrase

-
Non-polymers , 5 types, 1219 molecules

#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 39 / Source method: obtained synthetically / Formula: C2H6O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C4H10O3 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1156 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.31 Å3/Da / Density % sol: 46.76 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN I/F_PLUS/MINUS COLUMNS.
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M imidazole/hydrochloric acid buffer pH 8.5, 0.2 M calcium acetate , 10% (w/v) PEG 8000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Oct 21, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.43→48.73 Å / Num. obs: 80425 / % possible obs: 99.9 % / Redundancy: 6.9 % / Biso Wilson estimate: 24.4393052473 Å2 / CC1/2: 0.993 / Net I/σ(I): 7.4
Reflection shellResolution: 2.43→2.48 Å / Num. unique obs: 4541 / CC1/2: 0.827

-
Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5JBE

5jbe


Resolution: 2.4300227139→48.7263365866 Å / SU ML: 0.291604304582 / Cross valid method: FREE R-VALUE / σ(F): 1.34351629258 / Phase error: 29.4320367997
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.256481915017 3842 4.78861302224 %
Rwork0.193663259612 76390 -
obs0.196616983888 80232 99.5990317175 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 29.2621144871 Å2
Refinement stepCycle: LAST / Resolution: 2.4300227139→48.7263365866 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13246 0 252 1156 14654
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0070839702395613740
X-RAY DIFFRACTIONf_angle_d0.86570302099618588
X-RAY DIFFRACTIONf_chiral_restr0.0496951730492003
X-RAY DIFFRACTIONf_plane_restr0.004927897320862449
X-RAY DIFFRACTIONf_dihedral_angle_d12.62112322228077
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.430023-2.46080.3297531081251330.2568465512342841X-RAY DIFFRACTION99.4981599197
2.4608-2.49320.3191052375671580.2379104828672783X-RAY DIFFRACTION99.6949152542
2.4932-2.52730.3012050673161200.2374779068412834X-RAY DIFFRACTION99.3609149008
2.5273-2.56340.3002120127771600.229146940922787X-RAY DIFFRACTION99.8306233062
2.5634-2.60170.2828405921141490.2266627451052804X-RAY DIFFRACTION99.5952782462
2.6017-2.64230.300191548481500.2270279633662827X-RAY DIFFRACTION99.6318607764
2.6423-2.68560.3070953560161340.2289017957832790X-RAY DIFFRACTION99.6252129472
2.6856-2.73190.3263056431511610.2263195137662827X-RAY DIFFRACTION99.6664442962
2.7319-2.78160.3176905236141610.2238188909092803X-RAY DIFFRACTION99.5967741935
2.7816-2.83510.3278434633041330.2315995649692814X-RAY DIFFRACTION99.7292724196
2.8351-2.8930.3110845090471260.2244693698322846X-RAY DIFFRACTION99.7650218194
2.893-2.95590.315500962881090.2034465350512840X-RAY DIFFRACTION99.6620479892
2.9559-3.02460.2339813206831410.2051881182362837X-RAY DIFFRACTION99.6986943421
3.0246-3.10030.2432629639861460.2041396817622829X-RAY DIFFRACTION99.6649916248
3.1003-3.18410.2696381246491540.2000454977122804X-RAY DIFFRACTION99.8986828774
3.1841-3.27770.2784868899131460.2072723941912813X-RAY DIFFRACTION99.8313090418
3.2777-3.38350.2716394138061430.2033950328722862X-RAY DIFFRACTION100
3.3835-3.50440.2461001477141460.201972195392827X-RAY DIFFRACTION99.8991935484
3.5044-3.64470.2521272997141550.1871480461262839X-RAY DIFFRACTION99.8998998999
3.6447-3.81050.2404628395681440.1694561769962824X-RAY DIFFRACTION99.865410498
3.8105-4.01130.2235770003511350.1605342368832833X-RAY DIFFRACTION99.865410498
4.0113-4.26250.214699352851230.155425573882884X-RAY DIFFRACTION100
4.2625-4.59140.179800509121490.1494241804572836X-RAY DIFFRACTION99.9330431871
4.5914-5.0530.2063373015191490.1553233693872866X-RAY DIFFRACTION99.9337089824
5.053-5.78310.264777672571470.1695115088892843X-RAY DIFFRACTION99.7997329773
5.7831-7.28220.2106394406971440.1895849626882876X-RAY DIFFRACTION99.8677248677
7.2822-48.72633658660.2271178226981260.1895155213392821X-RAY DIFFRACTION95.5577172503

+
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