[English] 日本語
Yorodumi
- PDB-3vgh: Crystal structure of glycosyltrehalose trehalohydrolase (E283Q) c... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3vgh
TitleCrystal structure of glycosyltrehalose trehalohydrolase (E283Q) complexed with maltotriosyltrehalose
ComponentsMalto-oligosyltrehalose trehalohydrolase4-alpha-D-((1-4)-alpha-D-glucano)trehalose trehalohydrolase
KeywordsHYDROLASE / alpha/beta barrel / trehalose / trehalohydrolase / alpha-amylase
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
CITRATE ANION / Malto-oligosyltrehalose trehalohydrolase
Similarity search - Component
Biological speciesSulfolobus solfataricus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsOkazaki, N. / Tamada, T. / Feese, M.D. / Kato, M. / Miura, Y. / Komeda, T. / Kobayashi, K. / Kondo, K. / Kuroki, R.
CitationJournal: Protein Sci. / Year: 2012
Title: Substrate recognition mechanism of a glycosyltrehalose trehalohydrolase from Sulfolobus solfataricus KM1.
Authors: Okazaki, N. / Tamada, T. / Feese, M.D. / Kato, M. / Miura, Y. / Komeda, T. / Kobayashi, K. / Kondo, K. / Blaber, M. / Kuroki, R.
History
DepositionAug 9, 2011Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 20, 2012Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site_anisotrop.pdbx_label_asym_id / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Malto-oligosyltrehalose trehalohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,0356
Polymers64,7411
Non-polymers1,2945
Water2,936163
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Malto-oligosyltrehalose trehalohydrolase
hetero molecules

A: Malto-oligosyltrehalose trehalohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)132,07012
Polymers129,4822
Non-polymers2,58810
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area8080 Å2
ΔGint37 kcal/mol
Surface area40770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.801, 78.801, 282.704
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

-
Components

#1: Protein Malto-oligosyltrehalose trehalohydrolase / 4-alpha-D-((1-4)-alpha-D-glucano)trehalose trehalohydrolase / MTHase / 4-alpha-D-((1->4)-alpha-D-glucano)trehalose trehalohydrolase / Glycosyltrehalose ...MTHase / 4-alpha-D-((1->4)-alpha-D-glucano)trehalose trehalohydrolase / Glycosyltrehalose trehalohydrolase / GTHase / Maltooligosyl trehalose trehalohydrolase


Mass: 64740.754 Da / Num. of mol.: 1 / Mutation: E283Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus solfataricus (archaea) / Gene: treZ / Plasmid: PGUSS2 / Production host: Pichia jadinii (fungus)
References: UniProt: Q55088, 4-alpha-D-{(1->4)-alpha-D-glucano}trehalose trehalohydrolase
#2: Polysaccharide alpha-D-glucopyranose-(1-1)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D- ...alpha-D-glucopyranose-(1-1)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose


Type: oligosaccharide / Mass: 828.719 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpa1-1DGlcpa1-4DGlcpa1-4DGlcpa1-4DGlcpaGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,5,4/[a2122h-1a_1-5]/1-1-1-1-1/a1-b1_b4-c1_c4-d1_d4-e1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(1+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}}}}LINUCSPDB-CARE
#3: Chemical ChemComp-FLC / CITRATE ANION / Citric acid


Mass: 189.100 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5O7
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 163 / 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: 3.91 Å3/Da / Density % sol: 68.57 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 1.1M sodium citrate, 0.1M HEPES, 5mM MTT, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jan 24, 2001 / Details: mirrors
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→55.3 Å / Num. obs: 31666 / % possible obs: 97.9 % / Redundancy: 7.3 % / Rmerge(I) obs: 0.099 / Net I/σ(I): 13.2
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.296 / Mean I/σ(I) obs: 1.7 / % possible all: 81.7

-
Processing

Software
NameVersionClassificationNB
REFMACrefinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1EH9

1eh9


Resolution: 2.6→55.27 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.905 / WRfactor Rfree: 0.212 / WRfactor Rwork: 0.168 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8372 / SU B: 20.066 / SU ML: 0.192 / SU R Cruickshank DPI: 0.3451 / SU Rfree: 0.2605 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.26 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES
RfactorNum. reflection% reflectionSelection details
Rfree0.2441 1600 5.1 %RANDOM
Rwork0.1941 ---
obs0.1966 31605 97.69 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 108.31 Å2 / Biso mean: 45.7887 Å2 / Biso min: 16.16 Å2
Baniso -1Baniso -2Baniso -3
1-0.96 Å20.48 Å20 Å2
2--0.96 Å20 Å2
3----1.44 Å2
Refinement stepCycle: LAST / Resolution: 2.6→55.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4549 0 87 163 4799
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0224756
X-RAY DIFFRACTIONr_angle_refined_deg1.1341.9716426
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6495553
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.24624.449245
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.15615812
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.3741523
X-RAY DIFFRACTIONr_chiral_restr0.0830.2674
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0213632
X-RAY DIFFRACTIONr_mcbond_it0.3251.52751
X-RAY DIFFRACTIONr_mcangle_it0.63524450
X-RAY DIFFRACTIONr_scbond_it0.83932005
X-RAY DIFFRACTIONr_scangle_it1.4814.51976
LS refinement shellResolution: 2.601→2.669 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.322 93 -
Rwork0.3 1690 -
all-1783 -
obs--76.39 %
Refinement TLS params.Method: refined / Origin x: 11.7367 Å / Origin y: 33.686 Å / Origin z: 22.5008 Å
111213212223313233
T0.0179 Å20.0475 Å20.009 Å2-0.1712 Å20.0151 Å2--0.1329 Å2
L0.8892 °20.1198 °20.3078 °2-0.3967 °2-0.067 °2--1.8866 °2
S0.0286 Å °-0.0324 Å °0.0243 Å °-0.0055 Å °0.0064 Å °0.0251 Å °0.0064 Å °-0.2434 Å °-0.035 Å °

+
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