[English] 日本語
Yorodumi
- PDB-5jed: Apo-structure of humanised RadA-mutant humRadA28 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5jed
TitleApo-structure of humanised RadA-mutant humRadA28
ComponentsDNA repair and recombination protein RadA
KeywordsHYDROLASE / DNA repair / fragment based drug design / humanisation
Function / homology
Function and homology information


ATP-dependent DNA damage sensor activity / DNA recombination / damaged DNA binding / DNA repair / ATP hydrolysis activity / ATP binding
Similarity search - Function
DNA recombination/repair protein RadA / DNA recombination and repair protein, RecA-like / DNA recombination and repair protein Rad51-like, C-terminal / Rad51 / DNA recombination and repair protein RecA, monomer-monomer interface / RecA family profile 2. / DNA recombination and repair protein RecA-like, ATP-binding domain / RecA family profile 1. / DNA repair Rad51/transcription factor NusA, alpha-helical / Helix-hairpin-helix domain ...DNA recombination/repair protein RadA / DNA recombination and repair protein, RecA-like / DNA recombination and repair protein Rad51-like, C-terminal / Rad51 / DNA recombination and repair protein RecA, monomer-monomer interface / RecA family profile 2. / DNA recombination and repair protein RecA-like, ATP-binding domain / RecA family profile 1. / DNA repair Rad51/transcription factor NusA, alpha-helical / Helix-hairpin-helix domain / Helix-hairpin-helix DNA-binding motif, class 1 / Helix-hairpin-helix DNA-binding motif class 1 / P-loop containing nucleotide triphosphate hydrolases / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
DNA repair and recombination protein RadA
Similarity search - Component
Biological speciesPyrococcus furiosus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.332 Å
AuthorsFischer, G. / Marsh, M. / Moschetti, T. / Sharpe, T. / Scott, D. / Morgan, M. / Ng, H. / Skidmore, J. / Venkitaraman, A. / Abell, C. ...Fischer, G. / Marsh, M. / Moschetti, T. / Sharpe, T. / Scott, D. / Morgan, M. / Ng, H. / Skidmore, J. / Venkitaraman, A. / Abell, C. / Blundell, T.L. / Hyvonen, M.
CitationJournal: J.Mol.Biol. / Year: 2016
Title: Engineering Archeal Surrogate Systems for the Development of Protein-Protein Interaction Inhibitors against Human RAD51.
Authors: Moschetti, T. / Sharpe, T. / Fischer, G. / Marsh, M.E. / Ng, H.K. / Morgan, M. / Scott, D.E. / Blundell, T.L. / R Venkitaraman, A. / Skidmore, J. / Abell, C. / Hyvonen, M.
History
DepositionApr 18, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Oct 19, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 30, 2016Group: Database references
Revision 1.2Feb 7, 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: DNA repair and recombination protein RadA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,9965
Polymers25,6281
Non-polymers3684
Water3,621201
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area980 Å2
ΔGint-41 kcal/mol
Surface area10560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.771, 72.100, 41.927
Angle α, β, γ (deg.)90.00, 115.89, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein DNA repair and recombination protein RadA


Mass: 25628.178 Da / Num. of mol.: 1
Mutation: S167K, V168A, I169M, W170Y, I182L, K198D, H199N, I200V, Y201A, V202Y, L213Q, V215L, Q216Y, E219S, K221M, I222M, K223V, L225S, V232Y, K263R, H264F, A266R, D267M, L274E, Y275F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus (archaea) / Strain: ATCC 43587 / DSM 3638 / JCM 8422 / Vc1 / Gene: radA, PF1926 / Plasmid: pBAT4 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O74036

-
Non-polymers , 5 types, 205 molecules

#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Chemical ChemComp-MRD / (4R)-2-METHYLPENTANE-2,4-DIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 201 / 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 Å3/Da / Density % sol: 38.62 % / Description: rods
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 0.1M NaCacodylate pH=6.5, 5% PEG8000, 40% MPD

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.96862 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 13, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96862 Å / Relative weight: 1
ReflectionResolution: 1.332→37.72 Å / Num. obs: 45801 / % possible obs: 99.3 % / Redundancy: 4.7 % / CC1/2: 0.992 / Rmerge(I) obs: 0.093 / Rsym value: 0.103 / Net I/σ(I): 7.6
Reflection shellResolution: 1.332→1.337 Å / Redundancy: 3.2 % / Rmerge(I) obs: 1.086 / Mean I/σ(I) obs: 2.1 / % possible all: 99.1

-
Processing

Software
NameVersionClassification
REFMAC5.8.0124refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5j4l

5j4l


Resolution: 1.332→37.72 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.971 / SU B: 2.353 / SU ML: 0.041 / Cross valid method: THROUGHOUT / ESU R: 0.055 / ESU R Free: 0.052 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17122 2263 4.9 %RANDOM
Rwork0.13481 ---
obs0.13669 43497 99.14 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 21.216 Å2
Baniso -1Baniso -2Baniso -3
1--0.11 Å20 Å21.3 Å2
2---1.59 Å2-0 Å2
3---0.29 Å2
Refinement stepCycle: 1 / Resolution: 1.332→37.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1784 0 22 201 2007
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0191987
X-RAY DIFFRACTIONr_bond_other_d0.0020.021927
X-RAY DIFFRACTIONr_angle_refined_deg1.5791.9662706
X-RAY DIFFRACTIONr_angle_other_deg0.95834416
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0135263
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.87123.54893
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.98815348
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.1191518
X-RAY DIFFRACTIONr_chiral_restr0.0990.2300
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022359
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02481
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.8151.7341007
X-RAY DIFFRACTIONr_mcbond_other1.8131.7321006
X-RAY DIFFRACTIONr_mcangle_it2.2372.6141285
X-RAY DIFFRACTIONr_mcangle_other2.2362.6151286
X-RAY DIFFRACTIONr_scbond_it2.92.237980
X-RAY DIFFRACTIONr_scbond_other2.8992.24981
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.5043.1951422
X-RAY DIFFRACTIONr_long_range_B_refined4.29116.272342
X-RAY DIFFRACTIONr_long_range_B_other3.60215.5092258
X-RAY DIFFRACTIONr_rigid_bond_restr2.233914
X-RAY DIFFRACTIONr_sphericity_free32.218546
X-RAY DIFFRACTIONr_sphericity_bonded13.17554027
LS refinement shellResolution: 1.332→1.367 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.376 148 -
Rwork0.332 3201 -
obs--98.38 %

+
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