[English] 日本語
Yorodumi
- PDB-8pej: CjGH35 with a Galactosidase Activity-Based Probe -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8pej
TitleCjGH35 with a Galactosidase Activity-Based Probe
ComponentsBeta-galactosidase, putative, bgl35A
KeywordsHYDROLASE / Beta-galactosidase / Complex / Activity-based Probe
Function / homology
Function and homology information


beta-galactosidase complex / beta-galactosidase / beta-galactosidase activity / carbohydrate metabolic process
Similarity search - Function
Domain of unknown function DUF5597 / Domain of unknown function (DUF5597) / Glycoside hydrolase, family 42, N-terminal / Beta-galactosidase / Glycoside hydrolase superfamily
Similarity search - Domain/homology
ACETATE ION / Chem-YGX / Beta-galactosidase, putative, bgl35A
Similarity search - Component
Biological speciesCellvibrio japonicus Ueda107 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsOffen, W.A. / Davies, G.J.
Funding support United Kingdom, European Union, 2items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/R001162/1 United Kingdom
European Research Council (ERC)951231European Union
CitationJournal: Org.Biomol.Chem. / Year: 2023
Title: The development of a broad-spectrum retaining beta-exo-galactosidase activity-based probe.
Authors: Kuo, C.L. / Su, Q. / van den Nieuwendijk, A.M.C.H. / Beenakker, T.J.M. / Offen, W.A. / Willems, L.I. / Boot, R.G. / Sarris, A.J. / Marques, A.R.A. / Codee, J.D.C. / van der Marel, G.A. / ...Authors: Kuo, C.L. / Su, Q. / van den Nieuwendijk, A.M.C.H. / Beenakker, T.J.M. / Offen, W.A. / Willems, L.I. / Boot, R.G. / Sarris, A.J. / Marques, A.R.A. / Codee, J.D.C. / van der Marel, G.A. / Florea, B.I. / Davies, G.J. / Overkleeft, H.S. / Aerts, J.M.F.G.
History
DepositionJun 14, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 4, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Beta-galactosidase, putative, bgl35A
B: Beta-galactosidase, putative, bgl35A
C: Beta-galactosidase, putative, bgl35A
D: Beta-galactosidase, putative, bgl35A
E: Beta-galactosidase, putative, bgl35A
F: Beta-galactosidase, putative, bgl35A
G: Beta-galactosidase, putative, bgl35A
H: Beta-galactosidase, putative, bgl35A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)500,20165
Polymers497,0168
Non-polymers3,18557
Water79,5004413
1
A: Beta-galactosidase, putative, bgl35A
B: Beta-galactosidase, putative, bgl35A
C: Beta-galactosidase, putative, bgl35A
H: Beta-galactosidase, putative, bgl35A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)249,80726
Polymers248,5084
Non-polymers1,29922
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13110 Å2
ΔGint-183 kcal/mol
Surface area78390 Å2
MethodPISA
2
D: Beta-galactosidase, putative, bgl35A
E: Beta-galactosidase, putative, bgl35A
F: Beta-galactosidase, putative, bgl35A
G: Beta-galactosidase, putative, bgl35A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)250,39439
Polymers248,5084
Non-polymers1,88635
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14130 Å2
ΔGint-219 kcal/mol
Surface area78630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.316, 116.212, 116.396
Angle α, β, γ (deg.)90.236, 89.889, 90.094
Int Tables number1
Space group name H-MP1

-
Components

#1: Protein
Beta-galactosidase, putative, bgl35A


Mass: 62127.023 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Details: beta-galactosidase without signal peptide and with N-terminal hexahistidine tag
Source: (gene. exp.) Cellvibrio japonicus Ueda107 (bacteria)
Gene: bgl35A, CJA_2707 / Production host: Escherichia coli (E. coli) / References: UniProt: B3PBE0, beta-galactosidase
#2: Chemical...
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 35 / Source method: obtained synthetically / Formula: Na
#3: Chemical
ChemComp-YGX / (1~{S},2~{S},4~{S},5~{R})-6-(hydroxymethyl)cyclohexane-1,2,3,4,5-pentol


Mass: 194.182 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C7H14O6 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4413 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.71 Å3/Da / Density % sol: 54.57 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.4 / Details: Sodium acetate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97949 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 22, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.5→99.32 Å / Num. obs: 802827 / % possible obs: 96.3 % / Redundancy: 3.4 % / CC1/2: 0.997 / Rmerge(I) obs: 0.043 / Rpim(I) all: 0.043 / Rrim(I) all: 0.061 / Net I/σ(I): 10.4
Reflection shellResolution: 1.5→1.53 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.0467 / Mean I/σ(I) obs: 2 / Num. unique obs: 37248 / CC1/2: 0.719 / Rpim(I) all: 0.0467 / Rrim(I) all: 0.66 / % possible all: 90

-
Processing

Software
NameVersionClassification
REFMAC5.8.0411refinement
REFMAC5.8.0411refinement
Aimlessdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→82.544 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.968 / SU B: 1.198 / SU ML: 0.044 / Cross valid method: FREE R-VALUE / ESU R: 0.061 / ESU R Free: 0.063
Details: Hydrogens have been added in their riding positions There was incomplete electron density for loop 434 - 445, which has been modelled at partial occupancy or left partially unmodelled for each chain.
RfactorNum. reflection% reflection
Rfree0.181 40267 5.016 %
Rwork0.1566 762488 -
all0.158 --
obs-762488 96.256 %
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: 21.647 Å2
Baniso -1Baniso -2Baniso -3
1-1.202 Å2-0.143 Å20.182 Å2
2---0.43 Å20.126 Å2
3----0.771 Å2
Refinement stepCycle: LAST / Resolution: 1.5→82.544 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms33749 0 187 4413 38349
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.01235542
X-RAY DIFFRACTIONr_bond_other_d0.0010.01632682
X-RAY DIFFRACTIONr_angle_refined_deg1.7091.64948565
X-RAY DIFFRACTIONr_angle_other_deg0.5681.56775109
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.09454457
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.9865206
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.821105427
X-RAY DIFFRACTIONr_dihedral_angle_6_deg17.172101661
X-RAY DIFFRACTIONr_chiral_restr0.0890.25223
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0242424
X-RAY DIFFRACTIONr_gen_planes_other0.0010.028457
X-RAY DIFFRACTIONr_nbd_refined0.2280.26755
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1820.228690
X-RAY DIFFRACTIONr_nbtor_refined0.1850.217141
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.080.218084
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1740.23402
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0290.25
X-RAY DIFFRACTIONr_metal_ion_refined0.1150.248
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1890.243
X-RAY DIFFRACTIONr_nbd_other0.3060.2114
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.210.236
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.1010.27
X-RAY DIFFRACTIONr_mcbond_it1.9762.30517620
X-RAY DIFFRACTIONr_mcbond_other1.9742.30517607
X-RAY DIFFRACTIONr_mcangle_it2.6364.14122116
X-RAY DIFFRACTIONr_mcangle_other2.6364.14122117
X-RAY DIFFRACTIONr_scbond_it2.8612.47517922
X-RAY DIFFRACTIONr_scbond_other2.8612.47517923
X-RAY DIFFRACTIONr_scangle_it4.0934.44926442
X-RAY DIFFRACTIONr_scangle_other4.0934.44926443
X-RAY DIFFRACTIONr_lrange_it5.09524.71541430
X-RAY DIFFRACTIONr_lrange_other4.90323.78740048
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
1.5-1.5390.25328160.238528580.239616060.9530.95890.37110.239
1.539-1.5810.23428470.216537600.217602490.9620.96793.95510.215
1.581-1.6270.22328110.196529120.197584510.9660.97395.33280.192
1.627-1.6770.21527050.186515390.188567390.970.97895.60270.181
1.677-1.7320.225970.175502000.177550660.9750.98195.87950.169
1.732-1.7930.20625200.169486270.171532060.9730.98296.13010.163
1.793-1.860.20225480.163468920.165513670.9740.98396.24860.158
1.86-1.9360.19123800.161454280.163495390.9760.98396.50580.158
1.936-2.0220.19323860.159432940.161472470.9770.98496.68340.158
2.022-2.1210.18522350.155418210.157453360.9790.98597.17660.157
2.121-2.2360.17120420.148398740.149430870.9820.98797.28220.152
2.236-2.3710.17819080.146376690.148407750.980.98797.06190.153
2.371-2.5350.17318990.143355690.145382780.9810.98797.88390.154
2.535-2.7370.18517650.152332430.154356190.9790.98698.28460.167
2.737-2.9980.18516330.161307370.162328510.9790.98498.53580.18
2.998-3.3520.1814170.16276320.161295390.9820.98698.34120.18
3.352-3.8690.1613110.141246030.142261730.9850.98999.01040.166
3.869-4.7360.13710820.118207960.119220610.990.99299.17050.146
4.736-6.6870.1698970.156161330.156171190.9870.9999.48010.19
6.687-82.5440.2254690.21989010.21994060.9740.97599.61730.309

+
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