[English] 日本語
Yorodumi
- PDB-1eha: CRYSTAL STRUCTURE OF GLYCOSYLTREHALOSE TREHALOHYDROLASE FROM SULF... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1eha
TitleCRYSTAL STRUCTURE OF GLYCOSYLTREHALOSE TREHALOHYDROLASE FROM SULFOLOBUS SOLFATARICUS
ComponentsGLYCOSYLTREHALOSE TREHALOHYDROLASE
KeywordsHYDROLASE / trehalose / trehalohydrolase / Sulfolobus solfataricus / alpha-beta barrel / calcium binding / covalent dimer
Function / homology
Function and homology information


4-alpha-D-{(1->4)-alpha-D-glucano}trehalose trehalohydrolase / 4-alpha-D-(1->4)-alpha-D-glucanotrehalose trehalohydrolase activity / trehalose biosynthetic process / cytoplasm
Similarity search - Function
Malto-oligosyltrehalose trehalohydrolase, archaeal, C-terminal / Alpha-amylase, C terminal / Malto-oligosyltrehalose trehalohydrolase, E-set domain superfamily / Malto-oligosyltrehalose trehalohydrolase / Alpha amylase, catalytic domain / Glycosyl hydrolase, family 13, catalytic domain / Alpha-amylase domain / Golgi alpha-mannosidase II / Glycosyl hydrolase, all-beta / Glycosidases ...Malto-oligosyltrehalose trehalohydrolase, archaeal, C-terminal / Alpha-amylase, C terminal / Malto-oligosyltrehalose trehalohydrolase, E-set domain superfamily / Malto-oligosyltrehalose trehalohydrolase / Alpha amylase, catalytic domain / Glycosyl hydrolase, family 13, catalytic domain / Alpha-amylase domain / Golgi alpha-mannosidase II / Glycosyl hydrolase, all-beta / Glycosidases / Immunoglobulin E-set / Glycoside hydrolase superfamily / Immunoglobulins / TIM Barrel / Alpha-Beta Barrel / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Malto-oligosyltrehalose trehalohydrolase
Similarity search - Component
Biological speciesSulfolobus solfataricus (archaea)
MethodX-RAY DIFFRACTION / Isomorphous Replacement / Resolution: 3 Å
AuthorsFeese, M.D. / Kato, Y. / Tamada, T. / Kato, M. / Komeda, T. / Kobayashi, K. / Kuroki, R.
CitationJournal: J.Mol.Biol. / Year: 2000
Title: Crystal structure of glycosyltrehalose trehalohydrolase from the hyperthermophilic archaeum Sulfolobus solfataricus.
Authors: Feese, M.D. / Kato, Y. / Tamada, T. / Kato, M. / Komeda, T. / Miura, Y. / Hirose, M. / Hondo, K. / Kobayashi, K. / Kuroki, R.
History
DepositionFeb 19, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 19, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 14, 2018Group: Database references / Category: struct_ref_seq_dif / Item: _struct_ref_seq_dif.details
Revision 1.4Aug 9, 2023Group: 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: GLYCOSYLTREHALOSE TREHALOHYDROLASE


Theoretical massNumber of molelcules
Total (without water)64,7381
Polymers64,7381
Non-polymers00
Water54030
1
A: GLYCOSYLTREHALOSE TREHALOHYDROLASE

A: GLYCOSYLTREHALOSE TREHALOHYDROLASE


Theoretical massNumber of molelcules
Total (without water)129,4752
Polymers129,4752
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Unit cell
Length a, b, c (Å)80.366, 80.366, 281.998
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

-
Components

#1: Protein GLYCOSYLTREHALOSE TREHALOHYDROLASE / TREHALOHYDROLASE / GTHASE


Mass: 64737.723 Da / Num. of mol.: 1 / Mutation: C298V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus solfataricus (archaea) / Plasmid: PUCBG1 / Production host: Pichia jadinii (fungus) / References: UniProt: Q55088, alpha-amylase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 30 / 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: 4.1 Å3/Da / Density % sol: 69.7 %
Crystal growTemperature: 282 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.6-1.1 M sodium citrate 0.1 M HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 282K
Crystal grow
*PLUS
Temperature: 4 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110-20 mg/mlprotein1drop
20.6-1.1 Msodium citrate1drop
30.1 MHEPES1drop

-
Data collection

DiffractionMean temperature: 282 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Details: CHARLES SUPPER DOUBLE-MIRROR FOCUSING SYSTEM
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3→55.9 Å / Num. all: 93107 / Num. obs: 21534 / % possible obs: 93 % / Observed criterion σ(I): -3 / Redundancy: 4.3 % / Biso Wilson estimate: 36.6 Å2 / Rmerge(I) obs: 0.117 / Net I/σ(I): 11.6
Reflection shellResolution: 3→3.1 Å / Rmerge(I) obs: 0.666 / Mean I/σ(I) obs: 1.4 / % possible all: 73
Reflection
*PLUS
% possible obs: 93 % / Observed criterion σ(F): 2 / Num. measured all: 93107
Reflection shell
*PLUS
% possible obs: 73 %

-
Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
TNT5Erefinement
RefinementMethod to determine structure: Isomorphous Replacement
Starting model: 1EH9

1eh9


Resolution: 3→20 Å / Stereochemistry target values: Engh & Huber / Details: Conjugate direction
Num. reflection% reflectionSelection details
all21490 --
obs20393 93 %-
Rfree--CCP4 Uniqueify script
Solvent computationSolvent model: Moews and Kretsinger (1975) J. Mol. Biol., 91:201-228
Bsol: 608.444 Å2 / ksol: 0.914 e/Å3
Refinement stepCycle: LAST / Resolution: 3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4542 0 0 30 4572
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.01546611.15
X-RAY DIFFRACTIONt_angle_deg2.3662883
X-RAY DIFFRACTIONt_dihedral_angle_d23.35727220
X-RAY DIFFRACTIONt_trig_c_planes0.0141311.75
X-RAY DIFFRACTIONt_gen_planes0.0146707.7
X-RAY DIFFRACTIONt_nbd0.0233030
Software
*PLUS
Name: TNT / Version: 5E / Classification: refinement
Refinement
*PLUS
Highest resolution: 3 Å / Num. reflection Rfree: 1097 / % reflection Rfree: 5 % / Rfactor obs: 0.226 / Rfactor Rfree: 0.285 / Rfactor Rwork: 0.205
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev idealWeight
X-RAY DIFFRACTIONt_bond_d0.006
X-RAY DIFFRACTIONt_angle_deg1.8
X-RAY DIFFRACTIONt_planar_d0.0251.75
X-RAY DIFFRACTIONt_plane_restr0.0147.7
LS refinement shell
*PLUS
Highest resolution: 3 Å / Lowest resolution: 3.1 Å / Rfactor Rfree: 0.404 / Rfactor obs: 0.276

+
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