[English] 日本語
Yorodumi
- PDB-3vil: Crystal structure of beta-glucosidase from termite Neotermes kosh... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3vil
TitleCrystal structure of beta-glucosidase from termite Neotermes koshunensis in complex with salicin
ComponentsBeta-glucosidase
KeywordsHYDROLASE / CELLULASES / GLYCOSYL HYDROLASE
Function / homology
Function and homology information


: / beta-glucosidase / beta-glucosidase activity / carbohydrate metabolic process
Similarity search - Function
Glycoside hydrolase family 1, active site / Glycosyl hydrolases family 1 active site. / Glycosyl hydrolase family 1 / Glycoside hydrolase family 1 / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
2-(hydroxymethyl)phenyl beta-D-glucopyranoside / 2-(hydroxymethyl)phenol / Beta-glucosidase
Similarity search - Component
Biological speciesNeotermes koshunensis (cockroach)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.15 Å
AuthorsJeng, W.Y. / Liu, C.I. / Wang, A.H.J.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2012
Title: High-resolution structures of Neotermes koshunensis beta-glucosidase mutants provide insights into the catalytic mechanism and the synthesis of glucoconjugates
Authors: Jeng, W.Y. / Wang, N.C. / Lin, C.T. / Chang, W.J. / Liu, C.I. / Wang, A.H.J.
History
DepositionOct 3, 2011Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 4, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 26, 2013Group: Database references
Revision 1.2Jul 29, 2020Group: Data collection / Database references / Derived calculations
Category: chem_comp / pdbx_struct_conn_angle ...chem_comp / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.type ..._chem_comp.mon_nstd_flag / _chem_comp.type / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Nov 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: Beta-glucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,1507
Polymers55,5831
Non-polymers5666
Water12,052669
1


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

A: Beta-glucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,30014
Polymers111,1672
Non-polymers1,13312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1,y,-z1
Buried area2430 Å2
ΔGint-27 kcal/mol
Surface area32770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.908, 68.536, 75.663
Angle α, β, γ (deg.)90.00, 95.70, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-511-

CL

21A-512-

CL

-
Components

-
Protein / Sugars , 2 types, 2 molecules A

#1: Protein Beta-glucosidase


Mass: 55583.480 Da / Num. of mol.: 1 / Mutation: E193S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neotermes koshunensis (cockroach) / Gene: NkBG / Plasmid: pET-21a / Production host: Escherichia coli (E. coli) / Strain (production host): BL-21 (DE3) / References: UniProt: Q8T0W7, beta-glucosidase
#2: Sugar ChemComp-SA0 / 2-(hydroxymethyl)phenyl beta-D-glucopyranoside / Salicin / 2-(hydroxymethyl)phenyl beta-D-glucoside / 2-(hydroxymethyl)phenyl D-glucoside / 2-(hydroxymethyl)phenyl glucoside


Type: D-saccharide / Mass: 286.278 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C13H18O7

-
Non-polymers , 5 types, 674 molecules

#3: Chemical ChemComp-SA9 / 2-(hydroxymethyl)phenol


Mass: 124.137 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H8O2
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 669 / 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: 2.16 Å3/Da / Density % sol: 42.96 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1M Bis-Tris, 18-21%(w/v) PEG 3350, 0.1-0.25M MgCl2, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13C1 / Wavelength: 0.97622 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 22, 2010 / Details: Vertically Focusing Mirror
RadiationMonochromator: Horizontally Focusing Single Crystal Si(111) Bent Monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97622 Å / Relative weight: 1
ReflectionResolution: 1.15→30 Å / Num. all: 167114 / Num. obs: 166145 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 1 / Redundancy: 4.7 % / Biso Wilson estimate: 13.8 Å2 / Rmerge(I) obs: 0.046 / Net I/σ(I): 34.5
Reflection shellResolution: 1.15→1.19 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.458 / Mean I/σ(I) obs: 3.7 / Num. unique all: 16643 / % possible all: 99.7

-
Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3AHZ

3ahz


Resolution: 1.15→25.2 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.974 / SU B: 0.971 / SU ML: 0.02 / Isotropic thermal model: Isotropic with TLS / Cross valid method: THROUGHOUT / ESU R Free: 0.031 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.15428 8352 5 %RANDOM
Rwork0.12807 ---
obs0.12937 165967 99.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.59 Å2
Baniso -1Baniso -2Baniso -3
1--1.03 Å20 Å2-0.46 Å2
2---0.17 Å20 Å2
3---1.11 Å2
Refinement stepCycle: LAST / Resolution: 1.15→25.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3808 0 36 669 4513
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0224043
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4311.9435523
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.945499
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.84124.252214
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.66115632
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.2711523
X-RAY DIFFRACTIONr_chiral_restr0.0990.2572
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0213213
X-RAY DIFFRACTIONr_gen_planes_other
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_it1.3791.52386
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.98523856
X-RAY DIFFRACTIONr_scbond_it2.96331657
X-RAY DIFFRACTIONr_scangle_it4.214.51653
X-RAY DIFFRACTIONr_rigid_bond_restr1.42234043
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.15→1.212 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.235 1242 -
Rwork0.216 22871 -
obs-24113 99.31 %
Refinement TLS params.Method: refined / Origin x: -29.3385 Å / Origin y: 87.8597 Å / Origin z: 15.7032 Å
111213212223313233
T0.0173 Å20.0039 Å2-0.0006 Å2-0.0132 Å20.0006 Å2--0.0124 Å2
L0.4338 °2-0.0183 °20.0774 °2-0.189 °2-0.0583 °2--0.1967 °2
S-0.0117 Å °-0.0703 Å °-0.0186 Å °0.0302 Å °0.0145 Å °-0.0266 Å °-0.0125 Å °-0.0024 Å °-0.0028 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