[English] 日本語
Yorodumi
- PDB-7udi: Full-length dimer of DNA-Damage Response Protein C from Deinococc... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7udi
TitleFull-length dimer of DNA-Damage Response Protein C from Deinococcus radiodurans
ComponentsDNA damage response protein DdrC
KeywordsDNA BINDING PROTEIN / DNA Repair / Radioresistance
Biological speciesDeinococcus radiodurans (radioresistant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.24 Å
AuthorsSzabla, R. / Li, M.C. / Junop, M.S.
Funding support Canada, 1items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada)2008R00075 Canada
CitationJournal: Nucleic Acids Res. / Year: 2024
Title: DdrC, a unique DNA repair factor from D. radiodurans, senses and stabilizes DNA breaks through a novel lesion-recognition mechanism.
Authors: Szabla, R. / Li, M. / Warner, V. / Song, Y. / Junop, M.
History
DepositionMar 19, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 22, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond / pdbx_related_exp_data_set
Revision 1.2Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.3Jul 31, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.4Oct 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: DNA damage response protein DdrC
B: DNA damage response protein DdrC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,2006
Polymers50,8162
Non-polymers3844
Water72140
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Dimer in solution measured by SEC-MALS, homology, 3 crystal structures with different lattices interactions all contain this homodimer interface
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6800 Å2
ΔGint-112 kcal/mol
Surface area20220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.698, 66.698, 129.581
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number76
Space group name H-MP41
Space group name HallP4w
Symmetry operation#1: x,y,z
#2: -y,x,z+1/4
#3: y,-x,z+3/4
#4: -x,-y,z+1/2

-
Components

#1: Protein DNA damage response protein DdrC


Mass: 25407.971 Da / Num. of mol.: 2 / Mutation: L131M, L184M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Deinococcus radiodurans (radioresistant)
Plasmid: pDEST-527 / Details (production host): TEV-cleavable 6xHis tag (N-term) / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / Variant (production host): (DE3) T1R
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 40 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.84 Å3/Da / Density % sol: 56.63 % / Description: Elongated square bipyramid
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 250 uM DdrC 140 mM Sodium sulfate 14 mM Sodium citrate 3.6% (w/v) PEG 8000 4.3% (v/v) Pentaerythritol ethoxylate (3/4 EO/OH) 18 mM HEPES/NaOH, pH 7.5

-
Data collection

DiffractionMean temperature: 100 K / Ambient temp details: Nitrogen Cryo-stream / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08B1-1 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jan 13, 2022
Details: Incorporated white beam slits (WBS), a vertical collimating mirror (VCM), a double-crystal monochromator (DCM) / double-multilayer monochromator (DMM), and toroidal focusing mirror
RadiationMonochromator: KOHZU Si(111) double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.239→66.698 Å / Num. obs: 26343 / % possible obs: 96.8 % / Redundancy: 10.1 % / Biso Wilson estimate: 54.41 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.055 / Rpim(I) all: 0.023 / Rrim(I) all: 0.073 / Net I/σ(I): 19.1
Reflection shellResolution: 2.239→2.278 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.706 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 1335 / CC1/2: 0.631 / Rpim(I) all: 0.392 / Rrim(I) all: 0.899 / % possible all: 99.9

-
Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
autoPROC1.0.5data reduction
autoPROC1.0.5data scaling
AutoSol1.19.2_4158phasing
RefinementMethod to determine structure: SAD / Resolution: 2.24→59.3 Å / SU ML: 0.3187 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.0333
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2498 2512 4.85 %
Rwork0.2306 49260 -
obs0.2314 26336 96.29 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 66.54 Å2
Refinement stepCycle: LAST / Resolution: 2.24→59.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3233 0 20 40 3293
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.02093302
X-RAY DIFFRACTIONf_angle_d1.75134485
X-RAY DIFFRACTIONf_chiral_restr0.0949502
X-RAY DIFFRACTIONf_plane_restr0.0089598
X-RAY DIFFRACTIONf_dihedral_angle_d11.18451196
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.24-2.280.39981850.3522627X-RAY DIFFRACTION95.35
2.28-2.330.34271620.2982822X-RAY DIFFRACTION99.83
2.33-2.380.29961640.30032857X-RAY DIFFRACTION100
2.38-2.430.3581820.30232793X-RAY DIFFRACTION100
2.43-2.50.31371680.30272804X-RAY DIFFRACTION100
2.5-2.560.29261400.32082880X-RAY DIFFRACTION99.93
2.56-2.640.38231520.28942792X-RAY DIFFRACTION100
2.64-2.720.3737620.30751188X-RAY DIFFRACTION41.76
2.72-2.820.35921200.29352890X-RAY DIFFRACTION100
2.82-2.930.36171380.2762868X-RAY DIFFRACTION99.97
2.93-3.070.30621320.26412814X-RAY DIFFRACTION100
3.07-3.230.28341280.29392856X-RAY DIFFRACTION100
3.23-3.430.23081180.26622865X-RAY DIFFRACTION99.9
3.43-3.70.2803900.22452897X-RAY DIFFRACTION99.1
3.7-4.070.21431220.21352844X-RAY DIFFRACTION99.3
4.07-4.660.19311640.19552809X-RAY DIFFRACTION99.46
4.66-5.860.21521680.21262815X-RAY DIFFRACTION99.8
5.87-59.30.1991170.16842839X-RAY DIFFRACTION98.93

+
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