[English] 日本語
Yorodumi
- PDB-6tw4: HumRadA22F in complex with compound 6 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6tw4
TitleHumRadA22F in complex with compound 6
ComponentsDNA repair and recombination protein RadA
KeywordsDNA BINDING PROTEIN / RAD51 / RECOMBINASE / DNA REPAIR
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 / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Chem-NZW / DNA repair and recombination protein RadA
Similarity search - Component
Biological speciesPyrococcus furiosus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.73 Å
AuthorsMarsh, M.E. / Scott, D.E. / Coyne, A.G. / Skidmore, J. / Abell, C. / Hyvonen, M.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Wellcome Trust91050/Z/10/Z United Kingdom
Wellcome Trust080083/Z/06/Z United Kingdom
CitationJournal: Cell Chem Biol / Year: 2021
Title: A small-molecule inhibitor of the BRCA2-RAD51 interaction modulates RAD51 assembly and potentiates DNA damage-induced cell death.
Authors: Scott, D.E. / Francis-Newton, N.J. / Marsh, M.E. / Coyne, A.G. / Fischer, G. / Moschetti, T. / Bayly, A.R. / Sharpe, T.D. / Haas, K.T. / Barber, L. / Valenzano, C.R. / Srinivasan, R. / ...Authors: Scott, D.E. / Francis-Newton, N.J. / Marsh, M.E. / Coyne, A.G. / Fischer, G. / Moschetti, T. / Bayly, A.R. / Sharpe, T.D. / Haas, K.T. / Barber, L. / Valenzano, C.R. / Srinivasan, R. / Huggins, D.J. / Lee, M. / Emery, A. / Hardwick, B. / Ehebauer, M. / Dagostin, C. / Esposito, A. / Pellegrini, L. / Perrior, T. / McKenzie, G. / Blundell, T.L. / Hyvonen, M. / Skidmore, J. / Venkitaraman, A.R. / Abell, C.
History
DepositionJan 12, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 27, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jun 30, 2021Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first
Revision 1.3Jan 24, 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)27,2153
Polymers26,7141
Non-polymers5012
Water2,576143
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area100 Å2
ΔGint-12 kcal/mol
Surface area10830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.390, 60.150, 88.200
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein DNA repair and recombination protein RadA


Mass: 26714.355 Da / Num. of mol.: 1 / Fragment: humRadA22F
Mutation: S167K, V168A, I169M, W170Y, N175G, I182L, R183L, D192S, P193G D194S, E195D, K198D, H199N, I200V, Y201A, V202Y, L213Q, V215L, Q216Y, E219S, D220A, K221M, I222M, K223V, L225S, V232Y, K263R, ...Mutation: S167K, V168A, I169M, W170Y, N175G, I182L, R183L, D192S, P193G D194S, E195D, K198D, H199N, I200V, Y201A, V202Y, L213Q, V215L, Q216Y, E219S, D220A, K221M, I222M, K223V, L225S, V232Y, K263R, H264F, A266R, D267M, L274E, Y275F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1) (archaea)
Gene: radA, PF1926 / Plasmid: pBAT4 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O74036
#2: Chemical ChemComp-NZW / ~{N}-[2-[(2~{S})-2-[[(1~{S})-1-(4-methoxyphenyl)ethyl]carbamoyl]pyrrolidin-1-yl]-2-oxidanylidene-ethyl]quinoline-2-carboxamide


Mass: 460.525 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C26H28N4O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 143 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.11 Å3/Da / Density % sol: 41.68 % / Mosaicity: 0 °
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 6.5
Details: 20% PEG8000, 0.08 M Na Cacodylate pH 6.5, 0.16M Ca acetate, 18% glycerol

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 13, 2012 / Details: none
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 1.73→40.39 Å / Num. all: 23054 / Num. obs: 23054 / % possible obs: 99.6 % / Redundancy: 7.9 % / Biso Wilson estimate: 23.2 Å2 / Rpim(I) all: 0.035 / Rrim(I) all: 0.101 / Rsym value: 0.087 / Net I/av σ(I): 6.3 / Net I/σ(I): 15.2 / Num. measured all: 182953
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsRpim(I) allRrim(I) allRsym value% possible all
1.73-1.777.81.2550.631360.5021.4331.25598.6
1.77-1.828.10.970.731080.3781.1020.9799.8
1.82-1.888.10.8260.830060.3240.9430.82698.9
1.88-1.937.80.5671.229780.2280.650.56799.3
1.93-28.30.4371.628070.1670.4920.437100
2-2.078.30.341227690.1310.3840.34199.4
2.07-2.1580.2472.826610.0960.2780.24799.6
2.15-2.237.60.1943.625740.0790.2220.194100
2.23-2.338.20.1584.424540.0610.1790.15899.9
2.33-2.4580.1265.723340.050.1450.12699.8
2.45-2.5880.1126.522450.0450.1280.11299.9
2.58-2.748.30.0937.821260.0370.1070.093100
2.74-2.928.10.0799.119990.0310.0910.079100
2.92-3.167.60.06710.218650.0280.080.067100
3.16-3.468.20.05312.516980.0220.0630.053100
3.46-3.877.70.04613.215340.0190.0550.04699.9
3.87-4.4780.0415.313530.0160.0460.0499.9
4.47-5.477.30.03616.111520.0150.0420.03699.9
5.47-7.746.90.03715.58870.0170.0450.03799.7
7.74-40.395.60.0412.74850.0210.0520.0498.4

-
Processing

Software
NameVersionClassification
SCALA3.3.20data scaling
BUSTER2.10.0refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5J4L

5j4l


Resolution: 1.73→19.21 Å / Cor.coef. Fo:Fc: 0.9442 / Cor.coef. Fo:Fc free: 0.9304 / SU R Cruickshank DPI: 0.111 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.115 / SU Rfree Blow DPI: 0.108 / SU Rfree Cruickshank DPI: 0.106
RfactorNum. reflection% reflectionSelection details
Rfree0.2102 1171 5.09 %RANDOM
Rwork0.1784 ---
obs0.1801 22984 99.53 %-
Displacement parametersBiso max: 104.49 Å2 / Biso mean: 27.79 Å2 / Biso min: 10.88 Å2
Baniso -1Baniso -2Baniso -3
1-2.8635 Å20 Å20 Å2
2---4.9143 Å20 Å2
3---2.0507 Å2
Refine analyzeLuzzati coordinate error obs: 0.173 Å
Refinement stepCycle: final / Resolution: 1.73→19.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1751 0 35 143 1929
Biso mean--28.63 39.01 -
Num. residues----226
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d673SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes49HARMONIC2
X-RAY DIFFRACTIONt_gen_planes296HARMONIC5
X-RAY DIFFRACTIONt_it1842HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion239SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact2239SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d1842HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg2490HARMONIC21.09
X-RAY DIFFRACTIONt_omega_torsion3.48
X-RAY DIFFRACTIONt_other_torsion16.3
LS refinement shellResolution: 1.73→1.81 Å / Total num. of bins used: 12
RfactorNum. reflection% reflection
Rfree0.2155 146 5.36 %
Rwork0.1913 2580 -
all0.1926 2726 -
obs--99.53 %

+
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