[English] 日本語
Yorodumi
- PDB-5jta: Neutral trehalase Nth1 from Saccharomyces cerevisiae -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5jta
TitleNeutral trehalase Nth1 from Saccharomyces cerevisiae
ComponentsNeutral trehalase
KeywordsHYDROLASE / trehalase / glycosidase
Function / homology
Function and homology information


trehalase activity / alpha,alpha-trehalase / cellular response to desiccation / trehalose catabolic process / alpha,alpha-trehalase activity / calcium ion binding / cytoplasm
Similarity search - Function
Neutral trehalase Ca2+ binding / Neutral trehalase Ca2+ binding domain / Trehalase signature 1. / Glycoside hydrolase, family 37, conserved site / Trehalase signature 2. / Glycoside hydrolase, family 37 / Trehalase / Six-hairpin glycosidase-like superfamily / Six-hairpin glycosidase superfamily
Similarity search - Domain/homology
Cytosolic neutral trehalase
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.72 Å
AuthorsAlblova, M. / Smidova, A. / Obsilova, V. / Obsil, T.
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017
Title: Molecular basis of the 14-3-3 protein-dependent activation of yeast neutral trehalase Nth1.
Authors: Alblova, M. / Smidova, A. / Docekal, V. / Vesely, J. / Herman, P. / Obsilova, V. / Obsil, T.
History
DepositionMay 9, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Nov 1, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2017Group: Database references / Category: citation
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Nov 22, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 31, 2018Group: Data collection / Database references / Category: diffrn_source / pdbx_database_related
Item: _diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.pdbx_synchrotron_site / _diffrn_source.type
Revision 1.4May 1, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Neutral trehalase


Theoretical massNumber of molelcules
Total (without water)85,9891
Polymers85,9891
Non-polymers00
Water37821
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area22090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)186.700, 186.700, 119.870
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number180
Space group name H-MP6222

-
Components

#1: Protein Neutral trehalase / Alpha / alpha-trehalase / alpha-trehalose glucohydrolase


Mass: 85989.055 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: NTH1, NTH, YDR001C, YD8119.07C / Production host: Escherichia coli (E. coli) / References: UniProt: P32356, alpha,alpha-trehalase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 21 / 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: 3.51 Å3/Da / Density % sol: 64.92 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 7.3 / Details: Sodium Citrate, Ammonium Sulfate, Lithium Sulfate

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.918409 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 28, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918409 Å / Relative weight: 1
ReflectionResolution: 2.72→49.16 Å / Num. obs: 33613 / % possible obs: 99.9 % / Redundancy: 12.1 % / Biso Wilson estimate: 52.2 Å2 / Rrim(I) all: 0.187 / Net I/σ(I): 14.09
Reflection shellResolution: 2.72→2.88 Å / Mean I/σ(I) obs: 2.04 / Rrim(I) all: 1.29 / % possible all: 99.99

-
Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Preliminary model obtained from SAD experiment

Resolution: 2.72→48.15 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.896 / SU B: 0.002 / SU ML: 0 / Cross valid method: THROUGHOUT / ESU R: 0.217 / ESU R Free: 0.267 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2604 1680 5 %RANDOM
Rwork0.21102 ---
obs0.21345 31910 99.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 56.055 Å2
Baniso -1Baniso -2Baniso -3
1-1.85 Å20.93 Å20 Å2
2--1.85 Å20 Å2
3----6 Å2
Refinement stepCycle: 1 / Resolution: 2.72→48.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4379 0 0 21 4400
LS refinement shellResolution: 2.718→2.788 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.371 122 -
Rwork0.383 2314 -
obs--99.88 %

+
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