[English] 日本語
Yorodumi
- PDB-5fjs: Bacterial beta-glucosidase reveals the structural and functional ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5fjs
TitleBacterial beta-glucosidase reveals the structural and functional basis of genetic defects in human glucocerebrosidase 2 (GBA2)
ComponentsGLUCOSYLCERAMIDASE
KeywordsHYDROLASE / BILE ACID BETA-GLUCOSIDASE / GLUCOSYLCERAMIDASE / GBA2 / HEREDITARY ATAXIA
Function / homology
Function and homology information


glucosylceramidase / glucosylceramide catabolic process / glucosylceramidase 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
Biological speciesTHERMOANAEROBACTERIUM XYLANOLYTICUM (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsCharoenwattanasatien, R. / Pengthaisong, S. / Breen, I. / Mutoha, R. / Sansenya, S. / Hua, Y. / Tankrathok, A. / Wu, L. / Songsiriritthigul, C. / Tanaka, H. ...Charoenwattanasatien, R. / Pengthaisong, S. / Breen, I. / Mutoha, 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.
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. / Mutoha, 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. / Mutoha, 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
DepositionOct 12, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 11, 2016Provider: repository / Type: Initial release
Revision 1.1Jul 27, 2016Group: Database references
Revision 1.2Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: GLUCOSYLCERAMIDASE
B: GLUCOSYLCERAMIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)180,8134
Polymers180,7332
Non-polymers802
Water1,40578
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)187.974, 187.974, 99.075
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

-
Components

#1: Protein GLUCOSYLCERAMIDASE / / BETA-GLUCOSIDASE


Mass: 90366.602 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) THERMOANAEROBACTERIUM XYLANOLYTICUM (bacteria)
Strain: LX-11 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: F6BL85, beta-glucosidase
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 78 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsN TERMINAL SIGNAL SEQUENCE NOT INCLUDED IN CONSTRUCT

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.8 Å3/Da / Density % sol: 56 % / Description: NONE
Crystal growDetails: 0.2 M AMMONIUM SULFATE, 0.1 M BIS-TRIS PROPANE, PH 8, 15 % W/V PEG 6000.

-
Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.96862
DetectorType: DECTRIS PIXEL / Detector: PIXEL / Date: Apr 5, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96862 Å / Relative weight: 1
ReflectionResolution: 2.6→45.1 Å / Num. obs: 61406 / % possible obs: 100 % / Observed criterion σ(I): 1.7 / Redundancy: 10.3 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 15.9
Reflection shellResolution: 2.6→2.67 Å / Redundancy: 10.4 % / Rmerge(I) obs: 1.32 / Mean I/σ(I) obs: 1.7 / % possible all: 100

-
Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
MOSFLMdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 5BVU

5bvu


Resolution: 2.6→162.61 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.877 / SU B: 10.974 / SU ML: 0.233 / Cross valid method: THROUGHOUT / ESU R: 0.491 / ESU R Free: 0.308 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY. RESIDUES 21-34, 114-125, 804-806 DISORDERED FOR BOTH CHAINS A AND B. IN CHAIN A RESIDUES 134, 201-205, 223- - ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY. RESIDUES 21-34, 114-125, 804-806 DISORDERED FOR BOTH CHAINS A AND B. IN CHAIN A RESIDUES 134, 201-205, 223- -227, 240-242, 254, 297-302, 329, 428-431 ARE DISORDERED. IN CHAIN B RESIDUES 132-135, 166-169, 201-209, 222-228, 234-242, 248-249, 257-260, 275-279, 286-287, 294, 300-302, , 309, 314, 429-432 ARE DISORDERED. THERE IS UNMODELLED DENSITY BETWEEN RESIDUES 114-125, 200-206, 234-240 FOR CHAINS A AND B, BETWEEN RESIDUES 299-302 IN CHAIN A AND BETWEEN RESIDUES 132-135, 166-169 IN CHAIN B.
RfactorNum. reflection% reflectionSelection details
Rfree0.26649 3081 5 %RANDOM
Rwork0.20559 ---
obs0.20862 58306 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 58.022 Å2
Baniso -1Baniso -2Baniso -3
1--0.54 Å2-0.27 Å20 Å2
2---0.54 Å20 Å2
3---1.77 Å2
Refinement stepCycle: LAST / Resolution: 2.6→162.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11055 0 2 78 11135
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0211389
X-RAY DIFFRACTIONr_bond_other_d0.0020.029892
X-RAY DIFFRACTIONr_angle_refined_deg1.5611.92615483
X-RAY DIFFRACTIONr_angle_other_deg1.021322658
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.05451414
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.92924.716511
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.838151655
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.161522
X-RAY DIFFRACTIONr_chiral_restr0.0920.21594
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213164
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022752
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_it4.4766.1215715
X-RAY DIFFRACTIONr_mcbond_other4.4756.1215714
X-RAY DIFFRACTIONr_mcangle_it6.5949.1627099
X-RAY DIFFRACTIONr_mcangle_other6.5939.1637100
X-RAY DIFFRACTIONr_scbond_it4.2086.0435674
X-RAY DIFFRACTIONr_scbond_other4.2086.0445675
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.2359.0128382
X-RAY DIFFRACTIONr_long_range_B_refined8.3648.2713275
X-RAY DIFFRACTIONr_long_range_B_other8.35448.27613272
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.6→2.668 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.313 211 -
Rwork0.289 4284 -
obs--99.93 %

+
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