[English] 日本語
Yorodumi
- PDB-5ost: Beta-glucosidase from Thermoanaerobacterium xylolyticum GH116 in ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5ost
TitleBeta-glucosidase from Thermoanaerobacterium xylolyticum GH116 in complex with Gluco-1H-imidazole
ComponentsGlucosylceramidase
KeywordsHYDROLASE
Function / homology
Function and homology information


glucosylceramidase / glucosylceramide catabolic process / glucosylceramidase activity / beta-glucosidase activity / carbohydrate metabolic process / membrane / metal ion binding
Similarity search - Function
Glycosyl-hydrolase family 116, catalytic region / Beta-glucosidase GBA2-type / Glycosyl-hydrolase family 116, N-terminal / Glycosyl-hydrolase family 116, catalytic region / beta-glucosidase 2, glycosyl-hydrolase family 116 N-term / Six-hairpin glycosidase-like superfamily / Six-hairpin glycosidase superfamily / Prokaryotic membrane lipoprotein lipid attachment site profile.
Similarity search - Domain/homology
Chem-AEZ / Glucosylceramidase
Similarity search - Component
Biological speciesThermoanaerobacterium xylanolyticum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsDavies, G.J. / Offen, W.A.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
European Research CouncilERC-2012-AdG-322942 United Kingdom
CitationJournal: J. Am. Chem. Soc. / Year: 2018
Title: Gluco-1 H-imidazole: A New Class of Azole-Type beta-Glucosidase Inhibitor.
Authors: Schroder, S.P. / Wu, L. / Artola, M. / Hansen, T. / Offen, W.A. / Ferraz, M.J. / Li, K.Y. / Aerts, J.M.F.G. / van der Marel, G.A. / Codee, J.D.C. / Davies, G.J. / Overkleeft, H.S.
History
DepositionAug 18, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 11, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 25, 2018Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / citation ...chem_comp / citation / entity / pdbx_entity_nonpoly
Item: _chem_comp.name / _citation.journal_volume ..._chem_comp.name / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Revision 1.2May 9, 2018Group: Data collection / Structure summary / Category: struct / Item: _struct.title
Revision 1.3Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Glucosylceramidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,70816
Polymers91,7941
Non-polymers91415
Water4,828268
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2200 Å2
ΔGint-34 kcal/mol
Surface area25290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)177.617, 54.090, 83.559
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-910-

CL

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein Glucosylceramidase


Mass: 91794.180 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermoanaerobacterium xylanolyticum (strain ATCC 49914 / DSM 7097 / LX-11) (bacteria)
Gene: Thexy_2211 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: F6BL85, glucosylceramidase

-
Non-polymers , 5 types, 283 molecules

#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-AEZ / (4~{S},5~{S},6~{R},7~{R})-7-(hydroxymethyl)-4,5,6,7-tetrahydro-1~{H}-benzimidazole-4,5,6-triol


Mass: 200.192 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H12N2O4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 268 / 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: 2.53 Å3/Da / Density % sol: 51.4 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: PEG 3350, ammonium sulphate, Bis-tris

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.976 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 12, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 2.3→88.76 Å / Num. obs: 36706 / % possible obs: 99.9 % / Redundancy: 7.6 % / CC1/2: 0.949 / Rmerge(I) obs: 0.318 / Rpim(I) all: 0.126 / Net I/σ(I): 5.5
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 7.5 % / Rmerge(I) obs: 1.63 / Mean I/σ(I) obs: 2 / Num. unique obs: 3567 / CC1/2: 0.748 / Rpim(I) all: 0.64 / % possible all: 99.7

-
Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
DIALSdata reduction
Aimlessdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5BVU

5bvu


Resolution: 2.1→88.97 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.911 / SU B: 6.63 / SU ML: 0.166 / Cross valid method: THROUGHOUT / ESU R: 0.25 / ESU R Free: 0.204 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING. RESIDUES 429-431 ARE NOT MODELLED POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25094 2286 4.9 %RANDOM
Rwork0.19978 ---
obs0.20224 44762 98.07 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.56 Å2
Baniso -1Baniso -2Baniso -3
1--3.29 Å2-0 Å20 Å2
2--2.78 Å2-0 Å2
3---0.5 Å2
Refinement stepCycle: 1 / Resolution: 2.1→88.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6100 0 52 268 6420
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.026328
X-RAY DIFFRACTIONr_bond_other_d0.0020.025512
X-RAY DIFFRACTIONr_angle_refined_deg1.7111.9338581
X-RAY DIFFRACTIONr_angle_other_deg1.038312817
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.125761
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.65825.196306
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.442151009
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.1031513
X-RAY DIFFRACTIONr_chiral_restr0.1060.2871
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0217096
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021346
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.912.5753050
X-RAY DIFFRACTIONr_mcbond_other1.912.5753049
X-RAY DIFFRACTIONr_mcangle_it2.7863.8583809
X-RAY DIFFRACTIONr_mcangle_other2.7853.8583810
X-RAY DIFFRACTIONr_scbond_it1.9562.6613278
X-RAY DIFFRACTIONr_scbond_other1.9562.6613279
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.8943.9424773
X-RAY DIFFRACTIONr_long_range_B_refined4.30429.4817526
X-RAY DIFFRACTIONr_long_range_B_other4.30329.4817527
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.342 170 -
Rwork0.276 3255 -
obs--97.77 %

+
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