[English] 日本語
Yorodumi
- PDB-7oso: The crystal structure of Erwinia tasmaniensis levansucrase in com... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7oso
TitleThe crystal structure of Erwinia tasmaniensis levansucrase in complex with (S)-1,2,4-butanentriol
ComponentsLevansucrase (Beta-D-fructofuranosyl transferase)
KeywordsTRANSFERASE / fructosyltransferase / levan / FOS / transfructosylation / fructo-oligosaccharides / oligofructans
Function / homologylevansucrase / levansucrase activity / Glycoside hydrolase, family 68 / Levansucrase/Invertase / carbohydrate utilization / Glycosyl hydrolase, five-bladed beta-propellor domain superfamily / metal ion binding / (2~{S})-butane-1,2,4-triol / levansucrase
Function and homology information
Biological speciesErwinia tasmaniensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.4 Å
AuthorsPolsinelli, I. / Salomone-Stagni, M. / Benini, S.
Citation
Journal: Acta Crystallogr.,Sect.F / Year: 2022
Title: Erwinia tasmaniensis levansucrase shows enantiomer selection for (S)-1,2,4-butanetriol.
Authors: Polsinelli, I. / Salomone-Stagni, M. / Benini, S.
#1: Journal: Int J Mol Sci / Year: 2019
Title: The Structure of Sucrose-Soaked Levansucrase Crystals from Erwinia tasmaniensis reveals a Binding Pocket for Levanbiose.
Authors: Polsinelli, I. / Caliandro, R. / Demitri, N. / Benini, S.
#2: Journal: Int J Biol Macromol / Year: 2019
Title: Comparison of the Levansucrase from the epiphyte Erwinia tasmaniensis vs its homologue from the phytopathogen Erwinia amylovora.
Authors: Polsinelli, I. / Caliandro, R. / Salomone-Stagni, M. / Demitri, N. / Rejzek, M. / Field, R.A. / Benini, S.
History
DepositionJun 9, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 22, 2022Provider: repository / Type: Initial release
Revision 1.1Jul 5, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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 / _citation_author.identifier_ORCID
Revision 1.2Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Levansucrase (Beta-D-fructofuranosyl transferase)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,4425
Polymers46,1391
Non-polymers3024
Water9,314517
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, same as all levansucrases known to date
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area280 Å2
ΔGint-90 kcal/mol
Surface area16300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)127.713, 127.713, 61.016
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

-
Components

#1: Protein Levansucrase (Beta-D-fructofuranosyl transferase)


Mass: 46139.234 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Erwinia tasmaniensis (strain DSM 17950 / CIP 109463 / Et1/99) (bacteria)
Strain: DSM 17950 / CIP 109463 / Et1/99 / Gene: lsc, ETA_34670
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: B2VCC3, levansucrase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-0V1 / (2~{S})-butane-1,2,4-triol / (S)-1,2,4-butanentriol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 517 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.7 Å3/Da / Density % sol: 54.38 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: PEG 3000 15%, 1,2,4-Butanetriol (CAS 3068-00-6) 20%, NDSB 256 1%, 2.5 mM Manganese(II) chloride tetrahydrate, 2.5 mM Cobalt(II) chloride hexahydrate, 2.5 mM Nickel(II) chloride hexahydrate, ...Details: PEG 3000 15%, 1,2,4-Butanetriol (CAS 3068-00-6) 20%, NDSB 256 1%, 2.5 mM Manganese(II) chloride tetrahydrate, 2.5 mM Cobalt(II) chloride hexahydrate, 2.5 mM Nickel(II) chloride hexahydrate, 2.5 mM Zinc acetate dihydrate)

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Jul 20, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.4→45.19 Å / Num. obs: 189742 / % possible obs: 99.91 % / Redundancy: 5.6 % / Biso Wilson estimate: 20.95 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.05 / Net I/σ(I): 23.25
Reflection shellResolution: 1.4→1.45 Å / Num. unique obs: 30398 / CC1/2: 0.686

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassificationNB
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
REFMAC5.8.0258refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4D47

4d47


Resolution: 1.4→45.19 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.975 / SU B: 2.117 / SU ML: 0.035 / SU R Cruickshank DPI: 0.0474 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.047 / ESU R Free: 0.047 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1638 4939 5 %RANDOM
Rwork0.1326 ---
obs0.1342 94247 99.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 109.49 Å2 / Biso mean: 24.355 Å2 / Biso min: 15.31 Å2
Baniso -1Baniso -2Baniso -3
1--0.34 Å20 Å2-0 Å2
2---0.34 Å2-0 Å2
3---0.69 Å2
Refinement stepCycle: final / Resolution: 1.4→45.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3206 0 10 517 3733
Biso mean--25.86 41.83 -
Num. residues----412
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0133370
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172965
X-RAY DIFFRACTIONr_angle_refined_deg1.4681.6494613
X-RAY DIFFRACTIONr_angle_other_deg1.4251.5776885
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3465429
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.10522.588170
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.62115501
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.0621517
X-RAY DIFFRACTIONr_chiral_restr0.0780.2438
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023872
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02743
X-RAY DIFFRACTIONr_rigid_bond_restr1.8136334
LS refinement shellResolution: 1.4→1.436 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.361 335 -
Rwork0.332 6754 -
obs--97.5 %

+
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