[English] 日本語
Yorodumi
- PDB-5bx3: Crystal structure of Thermoanaerobacterium xylanolyticum GH116 be... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5bx3
TitleCrystal structure of Thermoanaerobacterium xylanolyticum GH116 beta-glucosidase with deoxynojirimycin
Componentsbeta-glucosidase
KeywordsHYDROLASE / Thermoanaerobacterium xylolyticum / GH116 / beta-glucosidase / deoxynojirimycin
Function / homology
Function and homology information


glucosylceramidase / glucosylceramide catabolic process / glucosylceramidase activity / beta-glucosidase activity / carbohydrate metabolic process / metal ion binding / membrane
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
1-DEOXYNOJIRIMYCIN / Glucosylceramidase
Similarity search - Component
Biological speciesThermoanaerobacterium xylanolyticum LX-11 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.96 Å
AuthorsCharoenwattanasatien, R. / Pengthaisong, S. / Sansenya, S. / Mutoh, R. / Tankrathok, A. / Tanaka, H. / Kurisu, G. / Ketudat Cairns, J.R.
Funding support Thailand, Japan, 3items
OrganizationGrant numberCountry
The Thailand Research FundBRG5680012 Thailand
Suranaree University of Technology, National Research University Project of the Commission on Higher Education of Thailand Thailand
Institute for Protein Research, Osaka University Japan
CitationJournal: Acs Chem.Biol. / Year: 2016
Title: Bacterial beta-Glucosidase Reveals the Structural and Functional Basis of Genetic Defects in Human Glucocerebrosidase 2 (GBA2)
Authors: Charoenwattanasatien, R. / Pengthaisong, S. / Breen, I. / Mutoh, R. / Sansenya, S. / Hua, Y. / Tankrathok, A. / Wu, L. / Songsiriritthigul, C. / Tanaka, H. / Williams, S.J. / Davies, G.J. / ...Authors: Charoenwattanasatien, R. / Pengthaisong, S. / Breen, I. / Mutoh, R. / Sansenya, S. / Hua, Y. / Tankrathok, A. / Wu, L. / Songsiriritthigul, C. / Tanaka, H. / Williams, S.J. / Davies, G.J. / Kurisu, G. / Ketudat Cairns, J.R.
History
DepositionJun 8, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 18, 2016Provider: repository / Type: Initial release
Revision 1.1Jul 27, 2016Group: Database references
Revision 1.2Feb 19, 2020Group: Data collection / Derived calculations / Category: diffrn_source / pdbx_struct_oper_list
Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Nov 8, 2023Group: 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: beta-glucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,44119
Polymers91,7941
Non-polymers1,64718
Water7,945441
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4390 Å2
ΔGint-9 kcal/mol
Surface area25660 Å2
Unit cell
Length a, b, c (Å)177.309, 54.662, 83.078
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein beta-glucosidase


Mass: 91794.180 Da / Num. of mol.: 1 / Fragment: UNP residues 19-806
Source method: isolated from a genetically manipulated source
Details: The author believe that the E.C. number and the enzyme name in UniProt F6BL85 is incorrect.
Source: (gene. exp.) Thermoanaerobacterium xylanolyticum LX-11 (bacteria)
Strain: LX-11 / Gene: Thexy_2211 / Plasmid: pET30a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: F6BL85, beta-glucosidase

-
Non-polymers , 5 types, 459 molecules

#2: Chemical ChemComp-NOJ / 1-DEOXYNOJIRIMYCIN / MORANOLINE


Mass: 163.172 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-CA / CALCIUM ION


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


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 441 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.21 Å3/Da / Density % sol: 44.43 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 0.14 M Ammonium Sulfate, 21% PEG 3000, 0.1 M MES

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Apr 22, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.96→50 Å / Num. obs: 58660 / % possible obs: 99.3 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.078 / Net I/σ(I): 28.4
Reflection shellResolution: 1.96→2.03 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.288 / Mean I/σ(I) obs: 10.2 / % possible all: 99.3

-
Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5BVU

5bvu


Resolution: 1.96→50 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.946 / SU B: 2.591 / SU ML: 0.076 / Cross valid method: THROUGHOUT / ESU R: 0.144 / ESU R Free: 0.124 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17679 2926 5 %RANDOM
Rwork0.14692 ---
obs0.14842 55692 99.18 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.599 Å2
Baniso -1Baniso -2Baniso -3
1--1.33 Å20 Å2-0 Å2
2--1.65 Å2-0 Å2
3----0.31 Å2
Refinement stepCycle: 1 / Resolution: 1.96→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6221 0 106 441 6768
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.026549
X-RAY DIFFRACTIONr_bond_other_d0.0010.025999
X-RAY DIFFRACTIONr_angle_refined_deg1.3481.9438855
X-RAY DIFFRACTIONr_angle_other_deg0.794313867
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2365781
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.70225.321312
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.746151096
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.9151512
X-RAY DIFFRACTIONr_chiral_restr0.0830.2901
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.027405
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021539
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_it1.1611.6693100
X-RAY DIFFRACTIONr_mcbond_other1.161.6693099
X-RAY DIFFRACTIONr_mcangle_it1.92.4953880
X-RAY DIFFRACTIONr_mcangle_other1.92.4963881
X-RAY DIFFRACTIONr_scbond_it1.6151.8923449
X-RAY DIFFRACTIONr_scbond_other1.6151.8923449
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.6622.7264973
X-RAY DIFFRACTIONr_long_range_B_refined4.94414.2518160
X-RAY DIFFRACTIONr_long_range_B_other4.79813.9838010
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.958→2.009 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2 188 -
Rwork0.156 3986 -
obs--97.64 %

+
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