[English] 日本語
Yorodumi
- PDB-8bar: E. coli C7 DarT1 in complex with ADP-ribosylated ssDNA and nicoti... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8bar
TitleE. coli C7 DarT1 in complex with ADP-ribosylated ssDNA and nicotinamide
Components
  • DNA (5'-D(*AP*AP*GP*AP*C)-3')
  • E. coli C7 DarT1
KeywordsTOXIN / TOXIN-ANTITOXIN / DNA ADP-RIBOSYLATION / ADP-ribosyltransferase activity / DNA binding
Function / homologyADENOSINE-5-DIPHOSPHORIBOSE / NICOTINAMIDE / DNA
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.63 Å
AuthorsSchuller, M. / Ariza, A.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/R007195/1 United Kingdom
CitationJournal: Mol.Cell / Year: 2023
Title: Molecular basis for the reversible ADP-ribosylation of guanosine bases.
Authors: Schuller, M. / Raggiaschi, R. / Mikolcevic, P. / Rack, J.G.M. / Ariza, A. / Zhang, Y. / Ledermann, R. / Tang, C. / Mikoc, A. / Ahel, I.
History
DepositionOct 11, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 12, 2023Provider: repository / Type: Initial release
Revision 1.1Jul 19, 2023Group: Data collection / Database references / Category: citation / diffrn_source
Item: _citation.journal_volume / _citation.page_first / _diffrn_source.pdbx_synchrotron_site
Revision 1.2Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / diffrn_source / pdbx_initial_refinement_model
Item: _diffrn_source.pdbx_synchrotron_site

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: E. coli C7 DarT1
D: DNA (5'-D(*AP*AP*GP*AP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,80911
Polymers25,6932
Non-polymers1,1169
Water6,413356
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4080 Å2
ΔGint15 kcal/mol
Surface area10260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.759, 61.759, 215.039
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

-
Components

-
Protein / DNA chain , 2 types, 2 molecules AD

#1: Protein E. coli C7 DarT1


Mass: 24180.104 Da / Num. of mol.: 1 / Mutation: E152A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: C3F40_23400 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta
#2: DNA chain DNA (5'-D(*AP*AP*GP*AP*C)-3')


Mass: 1513.051 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia coli (E. coli)

-
Non-polymers , 4 types, 365 molecules

#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-NCA / NICOTINAMIDE


Mass: 122.125 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H6N2O
#5: Chemical ChemComp-APR / ADENOSINE-5-DIPHOSPHORIBOSE


Mass: 559.316 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H23N5O14P2 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 356 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 4.0 M Sodium formate, 0.1 M Tris pH 7.5

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.976277 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: May 6, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976277 Å / Relative weight: 1
ReflectionResolution: 1.63→61.74 Å / Num. obs: 53204 / % possible obs: 100 % / Redundancy: 9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.072 / Rpim(I) all: 0.025 / Rrim(I) all: 0.076 / Net I/σ(I): 14
Reflection shellResolution: 1.63→1.66 Å / Redundancy: 9 % / Rmerge(I) obs: 1.581 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 2567 / CC1/2: 0.701 / Rpim(I) all: 0.551 / Rrim(I) all: 1.677 / % possible all: 100

-
Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7OMZ

7omz


Resolution: 1.63→46.832 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.972 / SU B: 2.764 / SU ML: 0.048 / Cross valid method: FREE R-VALUE / ESU R: 0.06 / ESU R Free: 0.062
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1779 2675 5.038 %
Rwork0.155 50422 -
all0.156 --
obs-53097 99.891 %
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: 24.661 Å2
Baniso -1Baniso -2Baniso -3
1-0.706 Å20 Å20 Å2
2--0.706 Å20 Å2
3----1.412 Å2
Refinement stepCycle: LAST / Resolution: 1.63→46.832 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1704 101 72 356 2233
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0121951
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161633
X-RAY DIFFRACTIONr_angle_refined_deg1.8891.6712665
X-RAY DIFFRACTIONr_angle_other_deg0.6241.5593825
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1975215
X-RAY DIFFRACTIONr_dihedral_angle_2_deg6.676511
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.33910293
X-RAY DIFFRACTIONr_dihedral_angle_6_deg17.7481097
X-RAY DIFFRACTIONr_chiral_restr0.0970.2285
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.022131
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02393
X-RAY DIFFRACTIONr_nbd_refined0.2230.2325
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1850.21536
X-RAY DIFFRACTIONr_nbtor_refined0.1910.2909
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0830.2959
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1820.2291
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2210.29
X-RAY DIFFRACTIONr_nbd_other0.2480.248
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.3130.230
X-RAY DIFFRACTIONr_mcbond_it1.8232.19839
X-RAY DIFFRACTIONr_mcbond_other1.8242.189838
X-RAY DIFFRACTIONr_mcangle_it2.4243.2761049
X-RAY DIFFRACTIONr_mcangle_other2.4233.2771050
X-RAY DIFFRACTIONr_scbond_it3.092.4841112
X-RAY DIFFRACTIONr_scbond_other3.0892.4851113
X-RAY DIFFRACTIONr_scangle_it4.4693.61612
X-RAY DIFFRACTIONr_scangle_other4.4683.6011613
X-RAY DIFFRACTIONr_lrange_it7.29236.2192396
X-RAY DIFFRACTIONr_lrange_other6.87432.0582267
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
1.63-1.6720.2872190.2935930.2938430.9360.93399.19330.29
1.672-1.7180.291850.26235810.26437670.9350.94899.97340.261
1.718-1.7680.2741910.2434590.24236500.9520.9611000.233
1.768-1.8220.2441790.21333790.21535580.9660.971000.203
1.822-1.8820.2331570.18832650.1934240.9710.97899.94160.176
1.882-1.9480.2121410.17632090.17733510.9730.9899.97020.161
1.948-2.0210.2051650.15730590.15932240.9770.9841000.141
2.021-2.1030.1781610.14429510.14631120.980.9871000.132
2.103-2.1970.1811440.14228700.14430140.9780.9871000.13
2.197-2.3040.1761190.13827570.1428770.9810.98899.96520.127
2.304-2.4280.1691490.13225790.13427360.9820.98999.70760.122
2.428-2.5750.1611180.13324980.13426180.9840.98999.92360.123
2.575-2.7520.161300.13823070.13924380.9840.98999.9590.131
2.752-2.9720.1791250.15121690.15322940.980.9861000.144
2.972-3.2540.1811240.16320130.16421380.9830.98699.95320.158
3.254-3.6360.1741080.15118460.15219550.9850.98899.94880.149
3.636-4.1940.144870.1216350.12117220.9890.9921000.118
4.194-5.1260.144790.12414180.12514970.9910.9931000.123
5.126-7.2070.19450.17811420.17811870.9830.9861000.176
7.207-46.8320.165490.2046920.2027470.9860.97499.19680.198
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.65350.0341-0.42560.85510.03050.96-0.0356-0.0473-0.01130.0640.0521-0.0307-0.00220.0782-0.01660.02360.01020.00630.0117-0.00010.0052-9.24528.151-34.0325
21.74720.0016-0.95610.42641.0673.19850.12170.10720.1657-0.11620.0605-0.039-0.34980.0768-0.18220.0752-0.01020.02840.01720.01110.0322-5.813220.7325-42.962
Refinement TLS groupSelection: ALL

+
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