[English] 日本語
Yorodumi
- PDB-5dfa: 3D structure of the E323A catalytic mutant of Gan42B, a GH42 beta... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5dfa
Title3D structure of the E323A catalytic mutant of Gan42B, a GH42 beta-galactosidase from G. stearothermophilus
ComponentsBeta-galactosidase
KeywordsHYDROLASE / Glycoside Hydrolase / Geobacillus stearothermophilus / Mutant Proteins / beta-Galactosidase
Function / homology
Function and homology information


galactose metabolic process / beta-galactosidase complex / beta-galactosidase / beta-galactosidase activity / metal ion binding
Similarity search - Function
Beta-galactosidase C-terminal / Beta-galactosidase C-terminal domain / Glycoside hydrolase, family 42 / Beta-galactosidase trimerisation / Beta-galactosidase trimerisation domain / Glycoside hydrolase, family 42, N-terminal / Beta-galactosidase / Class I glutamine amidotransferase (GATase) domain / Class I glutamine amidotransferase-like / Golgi alpha-mannosidase II ...Beta-galactosidase C-terminal / Beta-galactosidase C-terminal domain / Glycoside hydrolase, family 42 / Beta-galactosidase trimerisation / Beta-galactosidase trimerisation domain / Glycoside hydrolase, family 42, N-terminal / Beta-galactosidase / Class I glutamine amidotransferase (GATase) domain / Class I glutamine amidotransferase-like / Golgi alpha-mannosidase II / Glycosyl hydrolase, all-beta / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Immunoglobulin-like / Sandwich / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Biological speciesGeobacillus stearothermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsSolomon, H.V. / Tabachnikov, O. / Lansky, S. / Feinberg, H. / Govada, L. / Chayen, N.E. / Shoham, Y. / Shoham, G.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2015
Title: Structure-function relationships in Gan42B, an intracellular GH42 beta-galactosidase from Geobacillus stearothermophilus.
Authors: Solomon, H.V. / Tabachnikov, O. / Lansky, S. / Salama, R. / Feinberg, H. / Shoham, Y. / Shoham, G.
#1: Journal: Acta Crystallogr. Sect. F Struct. Biol. Cryst. Commun.
Year: 2013
Title: Crystallization and preliminary crystallographic analysis of GanB, a GH42 intracellular beta-galactosidase from Geobacillus stearothermophilus.
Authors: Solomon, H.V. / Tabachnikov, O. / Feinberg, H. / Govada, L. / Chayen, N.E. / Shoham, Y. / Shoham, G.
History
DepositionAug 26, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Dec 9, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 27, 2016Group: Database references
SupersessionMay 31, 2017ID: 4OJY
Revision 1.2May 31, 2017Group: Structure summary
Revision 1.3Jan 10, 2024Group: 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-galactosidase
B: Beta-galactosidase
C: Beta-galactosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)241,14615
Polymers240,1213
Non-polymers1,02512
Water20,1771120
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15930 Å2
ΔGint-57 kcal/mol
Surface area67240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.730, 181.310, 197.660
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Beta-galactosidase / Beta-gal


Mass: 80040.297 Da / Num. of mol.: 3 / Mutation: E323A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus stearothermophilus (bacteria)
Gene: ganB / Production host: Escherichia coli (E. coli) / References: UniProt: F8TRX0, beta-galactosidase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1120 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.67 Å3/Da / Density % sol: 54.01 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 16-18% PEG 3350, 250 mM NaCl, 100 mM Hepes buffer pH 7

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9763 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 19, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.5→71.7 Å / Num. obs: 87146 / % possible obs: 97.4 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.061 / Net I/σ(I): 13.9
Reflection shellResolution: 2.5→2.56 Å / Rmerge(I) obs: 0.198 / % possible all: 96.6

-
Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
DENZOdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1KWG

1kwg


Resolution: 2.5→66.806 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.13 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.22 4369 5.02 %
Rwork0.1573 --
obs0.1605 87099 96.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.5→66.806 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16921 0 57 1120 18098
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00217705
X-RAY DIFFRACTIONf_angle_d0.68324066
X-RAY DIFFRACTIONf_dihedral_angle_d13.3426513
X-RAY DIFFRACTIONf_chiral_restr0.0262498
X-RAY DIFFRACTIONf_plane_restr0.0033112
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.52840.27331530.17832696X-RAY DIFFRACTION96
2.5284-2.55820.29921590.17752710X-RAY DIFFRACTION96
2.5582-2.58940.30661450.17782706X-RAY DIFFRACTION97
2.5894-2.62210.25531390.17962736X-RAY DIFFRACTION97
2.6221-2.65660.30651410.18992792X-RAY DIFFRACTION97
2.6566-2.6930.28161520.19292697X-RAY DIFFRACTION98
2.693-2.73150.2621400.18252769X-RAY DIFFRACTION98
2.7315-2.77230.27121290.18042798X-RAY DIFFRACTION98
2.7723-2.81560.27051430.18172745X-RAY DIFFRACTION98
2.8156-2.86180.29051320.182788X-RAY DIFFRACTION98
2.8618-2.91110.24791310.17262780X-RAY DIFFRACTION98
2.9111-2.9640.24811460.17682769X-RAY DIFFRACTION98
2.964-3.02110.24131830.18012741X-RAY DIFFRACTION98
3.0211-3.08270.22971590.1672788X-RAY DIFFRACTION98
3.0827-3.14980.24931520.17172785X-RAY DIFFRACTION99
3.1498-3.2230.27831400.17412761X-RAY DIFFRACTION98
3.223-3.30360.21141430.16912805X-RAY DIFFRACTION98
3.3036-3.39290.24831370.16752797X-RAY DIFFRACTION98
3.3929-3.49280.21271580.16022747X-RAY DIFFRACTION98
3.4928-3.60550.21811320.15962816X-RAY DIFFRACTION98
3.6055-3.73440.21921410.15282765X-RAY DIFFRACTION97
3.7344-3.88390.18381560.14522724X-RAY DIFFRACTION97
3.8839-4.06060.1861520.13672772X-RAY DIFFRACTION97
4.0606-4.27460.18491190.13162796X-RAY DIFFRACTION97
4.2746-4.54240.16811480.12132721X-RAY DIFFRACTION95
4.5424-4.8930.16521580.1242740X-RAY DIFFRACTION96
4.893-5.38530.19521380.13532756X-RAY DIFFRACTION95
5.3853-6.1640.19091350.1592713X-RAY DIFFRACTION93
6.164-7.76420.20551500.15612699X-RAY DIFFRACTION91
7.7642-66.83010.16431580.1442818X-RAY DIFFRACTION91

+
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