[English] 日本語
Yorodumi
- PDB-5zqj: Crystal structure of beta-xylosidase from Bacillus pumilus -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5zqj
TitleCrystal structure of beta-xylosidase from Bacillus pumilus
ComponentsBeta-xylosidase
KeywordsHYDROLASE / xylobiose hydrolysis
Function / homology
Function and homology information


xylan 1,4-beta-xylosidase / xylan 1,4-beta-xylosidase activity / xylan catabolic process
Similarity search - Function
: / Beta-xylosidase, C-terminal Concanavalin A-like domain / Beta xylosidase C-terminal Concanavalin A-like domain / Glycoside hydrolase, family 43 / Glycosyl hydrolases family 43 / Glycosyl hydrolase domain; family 43 / 5 Propeller / Tachylectin-2; Chain A / Glycosyl hydrolase, five-bladed beta-propellor domain superfamily / Jelly Rolls - #200 ...: / Beta-xylosidase, C-terminal Concanavalin A-like domain / Beta xylosidase C-terminal Concanavalin A-like domain / Glycoside hydrolase, family 43 / Glycosyl hydrolases family 43 / Glycosyl hydrolase domain; family 43 / 5 Propeller / Tachylectin-2; Chain A / Glycosyl hydrolase, five-bladed beta-propellor domain superfamily / Jelly Rolls - #200 / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesBacillus pumilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.73 Å
AuthorsHa, N.C. / Hong, S. / Jo, I.
CitationJournal: Biochem. Biophys. Res. Commun. / Year: 2018
Title: Structure-based protein engineering of bacterial beta-xylosidase to increase the production yield of xylobiose from xylose
Authors: Hong, S. / Kyung, M. / Jo, I. / Kim, Y.R. / Ha, N.C.
History
DepositionApr 19, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 30, 2018Provider: repository / Type: Initial release
Revision 1.1Jun 6, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Beta-xylosidase
B: Beta-xylosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,7348
Polymers124,1812
Non-polymers5536
Water16,880937
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering, homodimer state (68% (w/w))
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5370 Å2
ΔGint-13 kcal/mol
Surface area37350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.261, 105.201, 105.814
Angle α, β, γ (deg.)90.00, 122.71, 90.00
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein Beta-xylosidase / 1 / 4-beta-D-xylan xylohydrolase / Xylan 1 / 4-beta-xylosidase


Mass: 62090.473 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus pumilus (bacteria) / Gene: xynB / Production host: Escherichia coli (E. coli) / References: UniProt: P07129, xylan 1,4-beta-xylosidase
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 937 / 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: 2.17 Å3/Da / Density % sol: 43.41 %
Crystal growTemperature: 287 K / Method: vapor diffusion, hanging drop
Details: 0.05M HEPES (pH 7.5), 20%(w/v) PEG 3350, 1%(w/v) tryptone

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9999 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 4, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9999 Å / Relative weight: 1
ReflectionResolution: 1.73→50 Å / Num. obs: 107503 / % possible obs: 97.5 % / Observed criterion σ(I): 0 / Redundancy: 4.7 % / Rmerge(I) obs: 0.08 / Rpim(I) all: 0.036 / Rrim(I) all: 0.088 / Χ2: 0.992 / Net I/σ(I): 17.23
Reflection shellResolution: 1.73→1.76 Å / Redundancy: 3 % / Rmerge(I) obs: 0.294 / Mean I/σ(I) obs: 2.63 / Num. unique obs: 5058 / CC1/2: 0.785 / Rpim(I) all: 0.18 / Rrim(I) all: 0.347 / Χ2: 0.767 / % possible all: 92.1

-
Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
DENZOdata reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1YIF

1yif


Resolution: 1.73→47.245 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.53 / Phase error: 17.83
RfactorNum. reflection% reflection
Rfree0.1882 4934 4.99 %
Rwork0.1545 --
obs0.1562 98865 89.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.73→47.245 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8654 0 36 937 9627
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0078956
X-RAY DIFFRACTIONf_angle_d0.87512172
X-RAY DIFFRACTIONf_dihedral_angle_d3.565214
X-RAY DIFFRACTIONf_chiral_restr0.0561263
X-RAY DIFFRACTIONf_plane_restr0.0061571
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7304-1.750.2487720.21231638X-RAY DIFFRACTION47
1.75-1.77060.25611110.19651856X-RAY DIFFRACTION53
1.7706-1.79220.23581080.19242033X-RAY DIFFRACTION59
1.7922-1.81490.20831330.20032205X-RAY DIFFRACTION63
1.8149-1.83880.22521610.20072311X-RAY DIFFRACTION68
1.8388-1.8640.23571450.20442540X-RAY DIFFRACTION73
1.864-1.89060.26071600.19292776X-RAY DIFFRACTION80
1.8906-1.91880.24071600.18712985X-RAY DIFFRACTION86
1.9188-1.94880.21361430.19063212X-RAY DIFFRACTION90
1.9488-1.98080.21221900.17453205X-RAY DIFFRACTION93
1.9808-2.01490.20292140.17633266X-RAY DIFFRACTION95
2.0149-2.05160.21021710.17443383X-RAY DIFFRACTION96
2.0516-2.0910.17811420.17693391X-RAY DIFFRACTION97
2.091-2.13370.24081730.17023398X-RAY DIFFRACTION97
2.1337-2.18010.23061960.16373426X-RAY DIFFRACTION98
2.1801-2.23080.21482000.16253396X-RAY DIFFRACTION97
2.2308-2.28660.19321840.15463434X-RAY DIFFRACTION98
2.2866-2.34840.19252020.15183443X-RAY DIFFRACTION99
2.3484-2.41750.19721550.16133450X-RAY DIFFRACTION99
2.4175-2.49560.19981890.15793460X-RAY DIFFRACTION99
2.4956-2.58470.19581580.15643523X-RAY DIFFRACTION99
2.5847-2.68820.21671630.15633479X-RAY DIFFRACTION99
2.6882-2.81060.19911840.16013481X-RAY DIFFRACTION99
2.8106-2.95870.20561690.15543478X-RAY DIFFRACTION99
2.9587-3.14410.18321760.15433490X-RAY DIFFRACTION100
3.1441-3.38670.18861540.14763535X-RAY DIFFRACTION100
3.3867-3.72740.16351690.13743529X-RAY DIFFRACTION100
3.7274-4.26650.14521870.12353492X-RAY DIFFRACTION100
4.2665-5.37420.13111920.12093515X-RAY DIFFRACTION100
5.3742-47.26290.16891730.15333601X-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