[English] 日本語
Yorodumi
- PDB-8ht0: Improved thermostability of a glucose-tolerant glycosidase based ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8ht0
TitleImproved thermostability of a glucose-tolerant glycosidase based on its X-ray crystal structure
ComponentsBeta-glucosidase
KeywordsHYDROLASE / glycosidase / crystal / thermostability
Function / homology
Function and homology information


: / beta-glucosidase / beta-glucosidase activity / cellulose catabolic process / cytosol
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 / Glycoside hydrolase superfamily
Similarity search - Domain/homology
Biological speciesCaldibacillus thermoamylovorans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsDong, P.P. / Wu, Y.K.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: Improved thermostability of a glucose-tolerant glycosidase based on its X-ray crystal structure
Authors: Dong, P.P. / Wu, Y.K.
History
DepositionDec 20, 2022Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Dec 20, 2023Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Beta-glucosidase


Theoretical massNumber of molelcules
Total (without water)51,9361
Polymers51,9361
Non-polymers00
Water6,864381
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)166.300, 166.300, 122.410
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422
Components on special symmetry positions
IDModelComponents
11A-814-

HOH

21A-836-

HOH

31A-843-

HOH

41A-853-

HOH

-
Components

#1: Protein Beta-glucosidase


Mass: 51936.414 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caldibacillus thermoamylovorans (bacteria)
Gene: CQJ30_16875 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A2U8EHQ1, beta-glucosidase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 381 / 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: 4.07 Å3/Da / Density % sol: 69.81 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop
Details: 0.1M Citric acid pH 4.0,1.4M Ammonium sulfate pH 5.0

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97915 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jan 6, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 1.96→43.16 Å / Num. obs: 61362 / % possible obs: 100 % / Redundancy: 26.4 % / CC1/2: 1 / Net I/σ(I): 21.3
Reflection shellResolution: 1.96→2.01 Å / Num. unique obs: 4500 / CC1/2: 0.671

-
Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
HKL-2000data reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→39.197 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 25.79 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2258 2863 4.96 %
Rwork0.1955 --
obs0.1971 57774 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→39.197 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3660 0 0 381 4041
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073772
X-RAY DIFFRACTIONf_angle_d0.8135112
X-RAY DIFFRACTIONf_dihedral_angle_d3.1012163
X-RAY DIFFRACTIONf_chiral_restr0.053510
X-RAY DIFFRACTIONf_plane_restr0.005663
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.03450.35031400.30222697X-RAY DIFFRACTION100
2.0345-2.07150.35531370.29822721X-RAY DIFFRACTION100
2.0715-2.11140.31431190.29582729X-RAY DIFFRACTION100
2.1114-2.15450.30331390.27212708X-RAY DIFFRACTION100
2.1545-2.20130.30181430.26282710X-RAY DIFFRACTION100
2.2013-2.25250.3191520.25712722X-RAY DIFFRACTION100
2.2525-2.30880.31771350.24832723X-RAY DIFFRACTION100
2.3088-2.37120.26261450.24812730X-RAY DIFFRACTION100
2.3712-2.4410.29151310.2432695X-RAY DIFFRACTION100
2.441-2.51980.24231580.23512729X-RAY DIFFRACTION100
2.5198-2.60980.26611570.22792725X-RAY DIFFRACTION100
2.6098-2.71430.24271410.22492737X-RAY DIFFRACTION100
2.7143-2.83780.28571310.22172747X-RAY DIFFRACTION100
2.8378-2.98730.28521370.23412743X-RAY DIFFRACTION100
2.9873-3.17440.23421410.20572759X-RAY DIFFRACTION100
3.1744-3.41940.22121690.1952725X-RAY DIFFRACTION100
3.4194-3.76330.20471510.16812762X-RAY DIFFRACTION100
3.7633-4.30720.17681450.14612779X-RAY DIFFRACTION100
4.3072-5.42440.16971350.14592828X-RAY DIFFRACTION100
5.4244-39.190.19491570.18242942X-RAY DIFFRACTION100

+
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