[English] 日本語
Yorodumi
- PDB-7wdo: Crystal structures of MeBglD2 in complex with various saccharides -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7wdo
TitleCrystal structures of MeBglD2 in complex with various saccharides
ComponentsBeta-glucosidase
KeywordsHYDROLASE / glycoside hydrolase family 1
Function / homology
Function and homology information


beta-glucosidase / beta-glucosidase activity / cellulose catabolic process
Similarity search - Function
Glycoside hydrolase, family 1, beta-glucosidase / Glycoside hydrolase family 1, active site / Glycosyl hydrolases family 1 active site. / Glycosyl hydrolases family 1, N-terminal conserved site / Glycosyl hydrolases family 1 N-terminal signature. / Glycosyl hydrolase family 1 / Glycoside hydrolase family 1 / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel ...Glycoside hydrolase, family 1, beta-glucosidase / Glycoside hydrolase family 1, active site / Glycosyl hydrolases family 1 active site. / Glycosyl hydrolases family 1, N-terminal conserved site / Glycosyl hydrolases family 1 N-terminal signature. / Glycosyl hydrolase family 1 / Glycoside hydrolase family 1 / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
beta-D-glucopyranose / beta-glucosidase
Similarity search - Component
Biological speciesmetagenome (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.21 Å
AuthorsWatanabe, M. / Matsuzawa, T. / Nakamichi, Y. / Akita, H. / Yaoi, K.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS) Japan
CitationJournal: Appl.Microbiol.Biotechnol. / Year: 2022
Title: Crystal structure of metagenomic beta-glycosidase MeBglD2 in complex with various saccharides
Authors: Matsuzawa, T. / Watanabe, M. / Nakamichi, Y. / Akita, H. / Yaoi, K.
History
DepositionDec 22, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 2, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Beta-glucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,9005
Polymers52,1851
Non-polymers7154
Water4,774265
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area210 Å2
ΔGint-16 kcal/mol
Surface area16430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)203.840, 203.840, 203.840
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number211
Space group name H-MI432

-
Components

#1: Protein Beta-glucosidase


Mass: 52185.109 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) metagenome (others) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1E1FFN6, beta-glucosidase
#2: Polysaccharide beta-D-glucopyranose-(1-4)-beta-D-glucopyranose


Type: oligosaccharide / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpb1-4DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(4+1)][b-D-Glcp]{}}LINUCSPDB-CARE
#3: Sugar ChemComp-BGC / beta-D-glucopyranose / beta-D-glucose / D-glucose / glucose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGlcpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-glucopyranoseCOMMON NAMEGMML 1.0
b-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 265 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.38 Å3/Da / Density % sol: 63.62 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1 M Tris-HCl buffer (pH 8.5), 1.2 M lithium sulfate, 0.01 M nickel chloride

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: May 19, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 36279 / % possible obs: 100 % / Redundancy: 20.7 % / Rmerge(I) obs: 0.101 / Net I/σ(I): 57.5
Reflection shellResolution: 2.2→2.24 Å / Rmerge(I) obs: 0.468 / Num. unique obs: 1767

-
Processing

Software
NameVersionClassification
REFMAC5.8.0349refinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5XGZ

5xgz


Resolution: 2.21→30.002 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.952 / WRfactor Rfree: 0.179 / WRfactor Rwork: 0.153 / SU B: 3.778 / SU ML: 0.096 / Average fsc free: 0.972 / Average fsc work: 0.9822 / Cross valid method: THROUGHOUT / ESU R: 0.167 / ESU R Free: 0.149
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflectionSelection details
Rfree0.1959 1868 5.154 %RANDOM
Rwork0.1623 34377 --
all0.164 ---
obs-36245 99.893 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 30.421 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.21→30.002 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3602 0 45 265 3912
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0123762
X-RAY DIFFRACTIONr_bond_other_d0.0410.0163217
X-RAY DIFFRACTIONr_angle_refined_deg1.6881.6475140
X-RAY DIFFRACTIONr_angle_other_deg1.121.5517480
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9645444
X-RAY DIFFRACTIONr_dihedral_angle_2_deg23.1591032
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.57710539
X-RAY DIFFRACTIONr_dihedral_angle_6_deg16.39910199
X-RAY DIFFRACTIONr_chiral_restr0.0790.2530
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.024376
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02836
X-RAY DIFFRACTIONr_nbd_refined0.220.2667
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1990.22652
X-RAY DIFFRACTIONr_nbtor_refined0.1840.21790
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0790.21830
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1510.2229
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.3420.28
X-RAY DIFFRACTIONr_nbd_other0.3840.216
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2040.24
X-RAY DIFFRACTIONr_mcbond_it2.953.1681779
X-RAY DIFFRACTIONr_mcbond_other2.9363.1691779
X-RAY DIFFRACTIONr_mcangle_it4.2744.7372222
X-RAY DIFFRACTIONr_mcangle_other4.2764.7412223
X-RAY DIFFRACTIONr_scbond_it3.9093.461983
X-RAY DIFFRACTIONr_scbond_other3.9083.461984
X-RAY DIFFRACTIONr_scangle_it5.5555.0682918
X-RAY DIFFRACTIONr_scangle_other5.5545.0682919
X-RAY DIFFRACTIONr_lrange_it7.00436.6264265
X-RAY DIFFRACTIONr_lrange_other7.00536.6274265
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.21-2.2670.2471370.19124910.19426310.9620.97799.8860.158
2.267-2.3290.2871340.20923980.21325330.9570.97499.96050.17
2.329-2.3960.2721270.1923760.19425030.9610.9781000.154
2.396-2.4690.2231250.18722900.18924150.970.9791000.149
2.469-2.550.2621300.18522210.18923510.9630.9791000.153
2.55-2.6390.2681270.18621540.1922830.9590.9899.91240.156
2.639-2.7370.2171310.1720680.17321990.9740.9831000.144
2.737-2.8480.1861180.15820170.1621380.9740.98599.85970.136
2.848-2.9740.209900.16119310.16320210.9750.9841000.143
2.974-3.1170.21060.16418440.16619510.9750.98399.94870.148
3.117-3.2840.191060.17717800.17718860.9760.9821000.163
3.284-3.480.216800.17916840.18117640.980.9821000.171
3.48-3.7170.1771100.1715590.17116690.9820.9841000.166
3.717-4.010.195620.15715110.15915730.9790.9871000.156
4.01-4.3850.169640.13413930.13614570.9870.991000.138
4.385-4.8890.123600.11912580.11913180.990.9921000.127
4.889-5.6210.156500.14211290.14211790.9860.9891000.15
5.621-6.8250.175550.1419720.14310270.9830.9881000.149
6.825-9.4110.151280.1397950.148230.9890.9881000.153
9.411-30.0020.156280.1825060.1815360.9840.98199.62690.22

+
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