[English] 日本語
Yorodumi
- PDB-2jg0: Family 37 trehalase from Escherichia coli in complex with 1- thia... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2jg0
TitleFamily 37 trehalase from Escherichia coli in complex with 1- thiatrehazolin
ComponentsPERIPLASMIC TREHALASE
KeywordsHYDROLASE / FAMILY 37 / INHIBITOR / TREHALASE / GLYCOSIDE HYDROLASE / PERIPLASMIC / GLYCOSIDASE / 1-THIATREHAZOLIN
Function / homology
Function and homology information


alpha,alpha-trehalase / alpha,alpha-trehalase activity / trehalose catabolic process / cellular hyperosmotic response / outer membrane-bounded periplasmic space / DNA damage response
Similarity search - Function
Trehalase, periplasmic / Trehalase signature 1. / Glycoside hydrolase, family 37, conserved site / Trehalase signature 2. / Trehalase / Glycoside hydrolase, family 37 / Glycosyltransferase - #10 / Six-hairpin glycosidase-like superfamily / Six-hairpin glycosidase superfamily / Glycosyltransferase ...Trehalase, periplasmic / Trehalase signature 1. / Glycoside hydrolase, family 37, conserved site / Trehalase signature 2. / Trehalase / Glycoside hydrolase, family 37 / Glycosyltransferase - #10 / Six-hairpin glycosidase-like superfamily / Six-hairpin glycosidase superfamily / Glycosyltransferase / Alpha/alpha barrel / Mainly Alpha
Similarity search - Domain/homology
Chem-TTZ / Periplasmic trehalase
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsGibson, R.P. / Gloster, T.M. / Roberts, S. / Warren, R.A.J. / Storch De Gracia, I. / Garcia, A. / Chiara, J.L. / Davies, G.J.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2007
Title: Molecular Basis for Trehalase Inhibition Revealed by the Structure of Trehalase in Complex with Potent Inhibitors.
Authors: Gibson, R.P. / Gloster, T.M. / Roberts, S. / Warren, R.A.J. / Storch De Gracia, I. / Garcia, A. / Chiara, J.L. / Davies, G.J.
History
DepositionFeb 7, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 13, 2007Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Jul 29, 2020Group: Atomic model / Derived calculations ...Atomic model / Derived calculations / Other / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / pdbx_database_status / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_label_atom_id / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Dec 13, 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
Revision 2.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: PERIPLASMIC TREHALASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,9092
Polymers60,5271
Non-polymers3821
Water12,178676
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)49.184, 101.719, 102.509
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein PERIPLASMIC TREHALASE / ALPHA ALPHA-TREHALASE / ALPHA ALPHA-TREHALOSE GLUCOHYDROLASE / TREHALASE


Mass: 60526.531 Da / Num. of mol.: 1 / Fragment: RESIDUES 31-565
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: K12 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: P13482, alpha,alpha-trehalase
#2: Sugar ChemComp-TTZ / N-[(3aS,4R,5S,6S,6aS)-4,5,6-trihydroxy-4-(hydroxymethyl)-4,5,6,6a-tetrahydro-3aH-cyclopenta[d][1,3]thiazol-2-yl]-alpha- D-glucopyranosylamine / N-[(3aS,4R,5S,6S,6aS)-4,5,6-trihydroxy-4-(hydroxymethyl)-4,5,6,6a-tetrahydro-3aH-cyclopenta[d][1,3]thiazol-2-yl]-alpha- D-glucosylamine / N-[(3aS,4R,5S,6S,6aS)-4,5,6-trihydroxy-4-(hydroxymethyl)-4,5,6,6a-tetrahydro-3aH-cyclopenta[d][1,3]thiazol-2-yl]-D-gluc osylamine / N-[(3aS,4R,5S,6S,6aS)-4,5,6-trihydroxy-4-(hydroxymethyl)-4,5,6,6a-tetrahydro-3aH-cyclopenta[d][1,3]thiazol-2-yl]-glucos ylamine


Type: D-saccharide / Mass: 382.387 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H22N2O9S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 676 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE FIRST 30 RESIDUES CORRESPOND TO A SIGNAL PEPTIDE THAT IS PREDICTED TO HAVE CLEAVED DURING ...THE FIRST 30 RESIDUES CORRESPOND TO A SIGNAL PEPTIDE THAT IS PREDICTED TO HAVE CLEAVED DURING EXPRESSION OF THE PROTEIN.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.2 Å3/Da / Density % sol: 43 %
Crystal growpH: 6.5
Details: 15 MG/ML PROTEIN, 25% PEG3350 AND 0.1 M BIS-TRIS HCL, PH 6.5.

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97377
DetectorType: ADSC CCD / Detector: CCD / Details: TOROIDAL MIRROR
RadiationMonochromator: SI(311) AND SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97377 Å / Relative weight: 1
ReflectionResolution: 1.5→30 Å / Num. obs: 83167 / % possible obs: 100 % / Redundancy: 5.3 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 12.6
Reflection shellResolution: 1.5→1.58 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 4 / % possible all: 100

-
Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PBD ENTRY 2JF4

2jf4


Resolution: 1.5→28.36 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.942 / SU B: 2.372 / SU ML: 0.042 / Cross valid method: THROUGHOUT / ESU R: 0.086 / ESU R Free: 0.072 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. NO ELECTRON DENSITY CAN BE OBSERVED FOR THE CHAIN BETWEEN 102 AND 107. THERE IS DISORDERED DENSITY IN THE REGION OF 478,546,547 WHICH HAS ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. NO ELECTRON DENSITY CAN BE OBSERVED FOR THE CHAIN BETWEEN 102 AND 107. THERE IS DISORDERED DENSITY IN THE REGION OF 478,546,547 WHICH HAS BEEN MODELLED AS BEST AS POSSIBLE.
RfactorNum. reflection% reflectionSelection details
Rfree0.189 4113 5 %RANDOM
Rwork0.147 ---
obs0.149 78956 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 8.5 Å2
Baniso -1Baniso -2Baniso -3
1--0.17 Å20 Å20 Å2
2--0.44 Å20 Å2
3----0.27 Å2
Refinement stepCycle: LAST / Resolution: 1.5→28.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4040 0 25 676 4741
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0224482
X-RAY DIFFRACTIONr_bond_other_d0.0020.023034
X-RAY DIFFRACTIONr_angle_refined_deg1.4771.9546182
X-RAY DIFFRACTIONr_angle_other_deg0.9463.0017451
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1215595
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.96524.756225
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.78215748
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.751526
X-RAY DIFFRACTIONr_chiral_restr0.0880.2664
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.025103
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02903
X-RAY DIFFRACTIONr_nbd_refined0.2260.21059
X-RAY DIFFRACTIONr_nbd_other0.2040.23524
X-RAY DIFFRACTIONr_nbtor_refined0.1890.22217
X-RAY DIFFRACTIONr_nbtor_other0.0890.22238
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1270.2411
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1150.226
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2470.257
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1470.277
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2041.52855
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.61924379
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.22232028
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.9974.51759
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.5→1.54 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.246 305
Rwork0.163 5792

+
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