[English] 日本語
Yorodumi
- PDB-8znw: Crystal structure of beta-glucosidase Cba3 from Cellulomonas biaz... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8znw
TitleCrystal structure of beta-glucosidase Cba3 from Cellulomonas biazotea in complex with glucose
ComponentsBeta-glucosidase
KeywordsHYDROLASE / glucosidase / Cellulomonas biazotea / glucose
Function / homology
Function and homology information


beta-glucosidase / beta-glucosidase activity / cellulose catabolic process / cytosol
Similarity search - Function
Glycoside hydrolase, family 1, beta-glucosidase / 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
beta-D-glucopyranose / Beta-glucosidase
Similarity search - Component
Biological speciesCellulomonas biazotea (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsKim, D. / Kim, I.J. / Nam, K.H.
Funding support Korea, Republic Of, 2items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)NRF-2021R1I1A1A01050838 Korea, Republic Of
National Research Foundation (NRF, Korea)NRF-2022R1I1A1A01072158 Korea, Republic Of
CitationJournal: To Be Published
Title: Crystal structure of beta-glucosidase Cba3 from Cellulomonas biazotea in complex with glucose
Authors: Kim, D. / Kim, I.J. / Nam, K.H.
History
DepositionMay 28, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 28, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Beta-glucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,3643
Polymers48,0031
Non-polymers3602
Water8,413467
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area380 Å2
ΔGint3 kcal/mol
Surface area15200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.080, 72.354, 78.381
Angle α, β, γ (deg.)90.00, 108.14, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-650-

HOH

21A-972-

HOH

31A-985-

HOH

41A-1050-

HOH

-
Components

#1: Protein Beta-glucosidase


Mass: 48003.324 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cellulomonas biazotea (bacteria) / Gene: cba3, bglB, CBZ_21620 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: G1C1T5, beta-glucosidase
#2: Sugar ChemComp-BGC / beta-D-glucopyranose / beta-D-glucose / D-glucose / glucose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 2 / Source method: isolated from a natural 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
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 467 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.44 Å3/Da / Density % sol: 49.67 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: Na-cacodylate, PEG 8000, calcium acetate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 11C / Wavelength: 0.9794 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 3, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 35911 / % possible obs: 98.6 % / Redundancy: 5.5 % / CC1/2: 0.964 / Net I/σ(I): 12.1
Reflection shellResolution: 1.9→1.93 Å / Num. unique obs: 1755 / CC1/2: 0.73

-
Processing

Software
NameVersionClassification
REFMAC5.8.0415refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→49.06 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.938 / SU B: 3.264 / SU ML: 0.091 / Cross valid method: THROUGHOUT / ESU R: 0.134 / ESU R Free: 0.121 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18783 1838 5.1 %RANDOM
Rwork0.1544 ---
obs0.15614 34073 98.31 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.915 Å2
Baniso -1Baniso -2Baniso -3
1-0.8 Å20 Å2-0.93 Å2
2---0.64 Å20 Å2
3---0.37 Å2
Refinement stepCycle: 1 / Resolution: 1.9→49.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3270 0 24 467 3761
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0123393
X-RAY DIFFRACTIONr_bond_other_d0.0010.0163050
X-RAY DIFFRACTIONr_angle_refined_deg1.5091.6594651
X-RAY DIFFRACTIONr_angle_other_deg0.5521.5787009
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4935426
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.516525
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.74610448
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.2490.2502
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.024141
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02805
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_it1.5861.6281710
X-RAY DIFFRACTIONr_mcbond_other1.5841.6281710
X-RAY DIFFRACTIONr_mcangle_it2.4842.9192134
X-RAY DIFFRACTIONr_mcangle_other2.4862.922135
X-RAY DIFFRACTIONr_scbond_it2.2651.7831683
X-RAY DIFFRACTIONr_scbond_other2.2641.7841684
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.6183.1852518
X-RAY DIFFRACTIONr_long_range_B_refined6.26417.844116
X-RAY DIFFRACTIONr_long_range_B_other5.84216.513921
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.95 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.252 126 -
Rwork0.23 2459 -
obs--95.6 %

+
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