[English] 日本語
Yorodumi
- PDB-2x6q: Crystal structure of trehalose synthase TreT from P.horikoshi -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2x6q
TitleCrystal structure of trehalose synthase TreT from P.horikoshi
ComponentsTREHALOSE-SYNTHASE TRET
KeywordsBIOSYNTHETIC PROTEIN
Function / homology
Function and homology information


alpha,alpha-trehalose synthase / trehalose synthase activity / glucose metabolic process
Similarity search - Function
: / Trehalose synthase, N-terminal domain / Glycosyl transferase, family 1 / Glycosyl transferases group 1 / Glycogen Phosphorylase B; / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesPYROCOCCUS HORIKOSHII (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsSong, H.-N. / Jung, T.-Y. / Yoon, S.-M. / Lim, M.-Y. / Lee, S.-B. / Woo, E.-J.
CitationJournal: J.Mol.Biol. / Year: 2010
Title: Structural Insights on the New Mechanism of Trehalose Synthesis by Trehalose Synthase Tret from Pyrococcus Horikoshii.
Authors: Woo, E.-J. / Ryu, S. / Song, H.-N. / Jung, T.-Y. / Yeon, S. / Lee, H. / Park, B.C. / Park, K. / Lee, S.-B.
History
DepositionFeb 19, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 13, 2010Provider: repository / Type: Initial release
Revision 1.1May 26, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: TREHALOSE-SYNTHASE TRET
B: TREHALOSE-SYNTHASE TRET


Theoretical massNumber of molelcules
Total (without water)96,4752
Polymers96,4752
Non-polymers00
Water4,900272
1
A: TREHALOSE-SYNTHASE TRET


Theoretical massNumber of molelcules
Total (without water)48,2381
Polymers48,2381
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: TREHALOSE-SYNTHASE TRET


Theoretical massNumber of molelcules
Total (without water)48,2381
Polymers48,2381
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)80.788, 63.655, 90.651
Angle α, β, γ (deg.)90.00, 99.41, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.999803, -0.010977, 0.01653), (0.010702, -0.999804, -0.016686), (0.01671, -0.016506, 0.999724)
Vector: 90.07294, 47.26453, -0.46063)

-
Components

#1: Protein TREHALOSE-SYNTHASE TRET / PUTATIVE UNCHARACTERIZED PROTEIN PH1035


Mass: 48237.551 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PYROCOCCUS HORIKOSHII (archaea) / Plasmid: P6XHIS119 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): MC1061 / References: UniProt: O58762
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 272 / 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: 2.34 Å3/Da / Density % sol: 46.6 % / Description: NONE
Crystal growDetails: PEG 3350 25%, 0.2M MGCL2, 0.1M SODIUM HEPES BUFFER

-
Data collection

DiffractionMean temperature: 297 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 4A / Wavelength: 1.2399
DetectorDate: Dec 1, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2399 Å / Relative weight: 1
ReflectionResolution: 2.2→29.99 Å / Num. obs: 41687 / % possible obs: 90.5 % / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Biso Wilson estimate: 18.9 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 16.4
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 3.95 / % possible all: 80.9

-
Processing

Software
NameVersionClassification
CNS1.2refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→29.99 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 335657.3 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.258 2077 5 %RANDOM
Rwork0.227 ---
obs0.227 41687 90.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 45.0601 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 32.6 Å2
Baniso -1Baniso -2Baniso -3
1-1.78 Å20 Å23.95 Å2
2---2.97 Å20 Å2
3---1.19 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.33 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.49 Å0.41 Å
Refinement stepCycle: LAST / Resolution: 2.2→29.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6711 0 0 272 6983
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.3
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.86
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it3.611.5
X-RAY DIFFRACTIONc_mcangle_it4.692
X-RAY DIFFRACTIONc_scbond_it5.672
X-RAY DIFFRACTIONc_scangle_it7.582.5
Refine LS restraints NCSNCS model details: RESTRAINTS / Rms dev position: 2.2 Å / Weight position: 29.99
LS refinement shellResolution: 2.2→2.34 Å / Rfactor Rfree error: 0.033 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.489 216 5 %
Rwork0.482 4096 -
obs--56.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2ION.PARAMION.TOP
X-RAY DIFFRACTION3WATER.PARAMWATER.TOP

+
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://pdbjlvh1.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