[English] 日本語
Yorodumi
- PDB-8z2u: Crystal structure of trehalose synthase mutamt E324D from Deinoco... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8z2u
TitleCrystal structure of trehalose synthase mutamt E324D from Deinococcus radiodurans complexed with validoxylamine A (VAA)
Componentsmaltose alpha-D-glucosyltransferase
KeywordsISOMERASE / trehalose
Function / homology
Function and homology information


maltose alpha-D-glucosyltransferase / maltose alpha-D-glucosyltransferase activity / carbohydrate metabolic process / metal ion binding
Similarity search - Function
Trehalose synthase/alpha-amylase, N-terminal / Maltogenic Amylase, C-terminal / Maltogenic Amylase, C-terminal domain / Oligo-1,6-glucosidase, domain 2 / Alpha amylase, catalytic domain / Glycosyl hydrolase, family 13, catalytic domain / Alpha-amylase domain / Glycosyl hydrolase, all-beta / Glycoside hydrolase superfamily
Similarity search - Domain/homology
Chem-VDM / maltose alpha-D-glucosyltransferase
Similarity search - Component
Biological speciesDeinococcus radiodurans (radioresistant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsYe, L.C. / Chen, S.C.
Funding support Taiwan, 1items
OrganizationGrant numberCountry
National Science Council (NSC, Taiwan) Taiwan
CitationJournal: J.Agric.Food Chem. / Year: 2024
Title: Structural and Mutational Analyses of Trehalose Synthase from Deinococcus radiodurans Reveal the Interconversion of Maltose-Trehalose Mechanism.
Authors: Ye, L.C. / Chow, S.Y. / Chang, S.C. / Kuo, C.H. / Wang, Y.L. / Wei, Y.J. / Lee, G.C. / Liaw, S.H. / Chen, W.M. / Chen, S.C.
History
DepositionApr 13, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 1, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: maltose alpha-D-glucosyltransferase
B: maltose alpha-D-glucosyltransferase
C: maltose alpha-D-glucosyltransferase
D: maltose alpha-D-glucosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)261,49416
Polymers259,8954
Non-polymers1,59912
Water00
1
A: maltose alpha-D-glucosyltransferase
C: maltose alpha-D-glucosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)130,7478
Polymers129,9482
Non-polymers7996
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4740 Å2
ΔGint-47 kcal/mol
Surface area36640 Å2
MethodPISA
2
B: maltose alpha-D-glucosyltransferase
D: maltose alpha-D-glucosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)130,7478
Polymers129,9482
Non-polymers7996
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4590 Å2
ΔGint-38 kcal/mol
Surface area36360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)134.731, 152.031, 153.213
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

-
Components

#1: Protein
maltose alpha-D-glucosyltransferase / Maltose alpha-D-glucosyltransferase


Mass: 64973.812 Da / Num. of mol.: 4 / Mutation: E324D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / CCUG 27074 / LMG 4051 / NBRC 15346 / NCIMB 9279 / VKM B-1422 / R1) (radioresistant)
Strain: ATCC 13939 / DSM 20539 / JCM 16871 / CCUG 27074 / LMG 4051 / NBRC 15346 / NCIMB 9279 / VKM B-1422 / R1
Production host: Escherichia coli (E. coli)
References: UniProt: I3NX86, maltose alpha-D-glucosyltransferase
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-VDM / (1S,2S,3R,6S)-4-(HYDROXYMETHYL)-6-{[(1S,2S,3S,4R,5R)-2,3,4-TRIHYDROXY-5-(HYDROXYMETHYL)CYCLOHEXYL]AMINO}CYCLOHEX-4-ENE-1,2,3-TRIOL / VALIDOXYLAMINE


Mass: 335.350 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C14H25NO8 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.02 Å3/Da / Density % sol: 59.26 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.2M Potassium sodium tartrate tetrahydrate and 20 % w/v Polyethylene glycol 3,350 (pH7.4)

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: TPS 05A / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Mar 1, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.9→30 Å / Num. obs: 63091 / % possible obs: 90.7 % / Redundancy: 5.2 % / Biso Wilson estimate: 28.66 Å2 / Rmerge(I) obs: 0.217 / Net I/σ(I): 8.6
Reflection shellResolution: 2.9→2.98 Å / Rmerge(I) obs: 0.197 / Num. unique obs: 59975

-
Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
HKL-2000data scaling
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→29.14 Å / SU ML: 0.4194 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.3161
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2521 3054 4.85 %
Rwork0.1801 59971 -
obs0.1836 63025 90.13 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 24.89 Å2
Refinement stepCycle: LAST / Resolution: 2.9→29.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17612 0 100 0 17712
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008818240
X-RAY DIFFRACTIONf_angle_d1.036724864
X-RAY DIFFRACTIONf_chiral_restr0.05582592
X-RAY DIFFRACTIONf_plane_restr0.01073280
X-RAY DIFFRACTIONf_dihedral_angle_d7.05292508
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9-2.950.36431250.27472750X-RAY DIFFRACTION91.44
2.95-30.37141560.26192733X-RAY DIFFRACTION91.66
3-3.050.35351390.2612714X-RAY DIFFRACTION91.77
3.05-3.110.31691350.25152734X-RAY DIFFRACTION91.66
3.11-3.160.38581510.23292746X-RAY DIFFRACTION91.53
3.16-3.230.32981320.22722741X-RAY DIFFRACTION91.12
3.23-3.30.27821100.21812749X-RAY DIFFRACTION91.31
3.3-3.380.33581150.22092758X-RAY DIFFRACTION90.83
3.38-3.460.30651410.20932706X-RAY DIFFRACTION90.81
3.46-3.550.26491430.19942726X-RAY DIFFRACTION90.71
3.55-3.660.24391290.17962733X-RAY DIFFRACTION90.83
3.66-3.780.22851560.16762718X-RAY DIFFRACTION90.81
3.78-3.910.22981410.16292718X-RAY DIFFRACTION90.36
3.91-4.070.24911430.15662718X-RAY DIFFRACTION90.34
4.07-4.250.21351290.14722724X-RAY DIFFRACTION89.86
4.25-4.470.18091740.13172683X-RAY DIFFRACTION90.13
4.48-4.750.21571410.13262720X-RAY DIFFRACTION89.57
4.75-5.120.1859970.13482734X-RAY DIFFRACTION89
5.12-5.630.21591400.1512741X-RAY DIFFRACTION89.06
5.63-6.440.21411630.14862666X-RAY DIFFRACTION87.83
6.44-8.080.23311320.16012708X-RAY DIFFRACTION87.28
8.08-29.140.18091620.15112751X-RAY DIFFRACTION85.73

+
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