[English] 日本語
Yorodumi
- PDB-6zj7: Trehalose transferase (TreT) from Thermoproteus uzoniensis soaked... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6zj7
TitleTrehalose transferase (TreT) from Thermoproteus uzoniensis soaked with Mg
ComponentsTrehalose phosphorylase/synthase
KeywordsTRANSFERASE / trehalose transferase / retaining glycosyltransferase / glycosidic bond formation
Function / homology: / Trehalose synthase, N-terminal domain / Glycosyl transferase, family 1 / Glycosyl transferases group 1 / glycosyltransferase activity / glucose metabolic process / THIOCYANATE ION / Trehalose phosphorylase/synthase
Function and homology information
Biological speciesThermoproteus uzoniensis (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsBento, I. / Mestrom, L. / Marsden, S.R. / van der Eijk, H. / Laustsen, J.U. / Jeffries, C.M. / Svergun, D.I. / Hagedoorn, P.-H. / Hanefeld, U.
Funding support Germany, 1items
OrganizationGrant numberCountry
European CommissionERA-IB-15-110 Germany
CitationJournal: Acs Catalysis / Year: 2020
Title: Anomeric Selectivity of Trehalose Transferase with Rare l-Sugars.
Authors: Mestrom, L. / Marsden, S.R. / van der Eijk, H. / Laustsen, J.U. / Jeffries, C.M. / Svergun, D.I. / Hagedoorn, P.L. / Bento, I. / Hanefeld, U.
History
DepositionJun 28, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 30, 2020Provider: repository / Type: Initial release
Revision 1.1May 1, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
AAA: Trehalose phosphorylase/synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,1148
Polymers45,5031
Non-polymers6117
Water1,58588
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1320 Å2
ΔGint-8 kcal/mol
Surface area16920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.574, 69.277, 110.451
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Trehalose phosphorylase/synthase


Mass: 45503.316 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermoproteus uzoniensis (strain 768-20) (archaea)
Strain: 768-20 / Gene: TUZN_0976 / Production host: Escherichia coli (E. coli) / References: UniProt: F2L613
#2: Chemical
ChemComp-SCN / THIOCYANATE ION


Mass: 58.082 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: CNS
#3: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 88 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.55 Å3/Da / Density % sol: 51.7 %
Crystal growTemperature: 292 K / Method: vapor diffusion / pH: 6.5
Details: Bis-Tris Propane, PEG 3350, potassium thiocyanate, PEG 400

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 2, 2019
RadiationMonochromator: double-crystal monochromator FMB-OXFORD (Oxford, UK)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.15→110.45 Å / Num. obs: 25646 / % possible obs: 98.8 % / Redundancy: 7.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.07 / Rpim(I) all: 0.039 / Rrim(I) all: 0.081 / Net I/σ(I): 17.1
Reflection shellResolution: 2.15→2.21 Å / Redundancy: 8.1 % / Rmerge(I) obs: 0.024 / Num. unique obs: 2477 / CC1/2: 0.7 / Rpim(I) all: 0.013 / Rrim(I) all: 0.028

-
Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
REFMAC5.8.0258refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: apo-TreT

Resolution: 2.15→58.757 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.935 / WRfactor Rfree: 0.257 / WRfactor Rwork: 0.193 / SU B: 7.635 / SU ML: 0.188 / Average fsc free: 0.862 / Average fsc work: 0.8837 / Cross valid method: FREE R-VALUE / ESU R: 0.237 / ESU R Free: 0.211
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2612 1311 5.112 %
Rwork0.1985 24335 -
all0.202 --
obs-25646 98.779 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 52.554 Å2
Baniso -1Baniso -2Baniso -3
1-3.601 Å20 Å2-0 Å2
2---2.509 Å20 Å2
3----1.092 Å2
Refinement stepCycle: LAST / Resolution: 2.15→58.757 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3162 0 37 88 3287
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0133281
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173142
X-RAY DIFFRACTIONr_angle_refined_deg1.2991.6444431
X-RAY DIFFRACTIONr_angle_other_deg1.1511.5787269
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6455395
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.39321.006179
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.68815572
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2981528
X-RAY DIFFRACTIONr_chiral_restr0.0560.2412
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023611
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02709
X-RAY DIFFRACTIONr_nbd_refined0.1950.2622
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1730.22965
X-RAY DIFFRACTIONr_nbtor_refined0.1580.21505
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0710.21647
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1450.2115
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.210.25
X-RAY DIFFRACTIONr_nbd_other0.170.236
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1180.26
X-RAY DIFFRACTIONr_mcbond_it3.2685.3581578
X-RAY DIFFRACTIONr_mcbond_other3.2625.3571573
X-RAY DIFFRACTIONr_mcangle_it4.9278.0261965
X-RAY DIFFRACTIONr_mcangle_other4.9268.0271966
X-RAY DIFFRACTIONr_scbond_it3.545.841703
X-RAY DIFFRACTIONr_scbond_other3.5395.841704
X-RAY DIFFRACTIONr_scangle_it5.7678.562464
X-RAY DIFFRACTIONr_scangle_other5.7668.562465
X-RAY DIFFRACTIONr_lrange_it7.80861.343530
X-RAY DIFFRACTIONr_lrange_other7.81461.2783519
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.15-2.2060.348960.3021754X-RAY DIFFRACTION98.2475
2.206-2.2660.295970.2861685X-RAY DIFFRACTION98.0738
2.266-2.3320.295790.2651710X-RAY DIFFRACTION98.0274
2.332-2.4040.336790.2391633X-RAY DIFFRACTION98.2778
2.404-2.4830.315840.2421566X-RAY DIFFRACTION98.4487
2.483-2.570.323830.2221541X-RAY DIFFRACTION98.6035
2.57-2.6670.32720.2221474X-RAY DIFFRACTION98.6599
2.667-2.7750.256830.2031447X-RAY DIFFRACTION98.9651
2.775-2.8990.272680.191376X-RAY DIFFRACTION98.9041
2.899-3.040.254860.2031299X-RAY DIFFRACTION99.212
3.04-3.2040.3640.2191253X-RAY DIFFRACTION99.2464
3.204-3.3990.286710.2211198X-RAY DIFFRACTION99.2181
3.399-3.6330.273510.2021142X-RAY DIFFRACTION99.3339
3.633-3.9240.259640.1951045X-RAY DIFFRACTION99.3728
3.924-4.2980.235480.166986X-RAY DIFFRACTION99.3276
4.298-4.8040.217380.155905X-RAY DIFFRACTION99.2632
4.804-5.5450.181540.159784X-RAY DIFFRACTION98.9374
5.545-6.7870.311300.19683X-RAY DIFFRACTION99.4421
6.787-9.5810.207360.162536X-RAY DIFFRACTION99.6516

+
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