[English] 日本語
Yorodumi
- PDB-6tv3: HumRadA1 in complex with 3-amino-2-naphthoic acid -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6tv3
TitleHumRadA1 in complex with 3-amino-2-naphthoic acid
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
3-azanylnaphthalene-2-carboxylic acid / PHOSPHATE ION / DNA repair and recombination protein RadA
Similarity search - Component
Biological speciesPyrococcus furiosus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsMarsh, M.E. / 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 8, 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)25,9695
Polymers25,5021
Non-polymers4664
Water3,981221
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area660 Å2
ΔGint-7 kcal/mol
Surface area10490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.666, 79.237, 39.430
Angle α, β, γ (deg.)90.000, 118.180, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein DNA repair and recombination protein RadA


Mass: 25502.150 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus (archaea) / Gene: radA, PF1926 / Details (production host): pBAT4 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O74036
#2: Chemical ChemComp-NYE / 3-azanylnaphthalene-2-carboxylic acid


Mass: 187.195 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H9NO2
#3: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 221 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.03 Å3/Da / Density % sol: 39.52 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6.5 / Details: 8% PEG-1000, 100 MM NA/K PHOSPHATE

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 8, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.5→21.03 Å / Num. obs: 31934 / % possible obs: 97.4 % / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Biso Wilson estimate: 18.52 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.049 / Rrim(I) all: 0.061 / Χ2: 0.907 / Net I/σ(I): 15.9 / Num. measured all: 116392
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.5-1.593.60.452.9180341039688120.870.53996.4
1.59-1.72.0590.2493.4417580987285390.8890.33286.5
1.7-1.842.0770.1445.6616522904979560.9560.19487.9
1.84-2.012.0770.089.4815581843575030.9840.10989
2.01-2.252.0590.05314.0314054760168250.9910.07289.8
2.25-2.592.0310.03918.1712345671860780.9940.05490.5
2.59-3.171.990.03421.1510316568551830.9950.04691.2
3.17-4.461.9510.0324.67694440239440.9960.04289.6
4.46-21.031.9540.02925.624266246821830.9960.04188.5

-
Processing

Software
NameVersionClassification
XSCALEdata scaling
BUSTER2.10.3refinement
PDB_EXTRACT3.23data extraction
XDSdata reduction
Cootmodel building
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4b32

4b32


Resolution: 1.5→21.03 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.928 / SU R Cruickshank DPI: 0.08 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.083 / SU Rfree Blow DPI: 0.084 / SU Rfree Cruickshank DPI: 0.082
RfactorNum. reflection% reflectionSelection details
Rfree0.217 1647 5.18 %RANDOM
Rwork0.183 ---
obs0.185 31812 97.5 %-
Displacement parametersBiso max: 99.96 Å2 / Biso mean: 24.48 Å2 / Biso min: 7.07 Å2
Baniso -1Baniso -2Baniso -3
1-1.2041 Å20 Å2-2.1697 Å2
2---2.3176 Å20 Å2
3---1.1135 Å2
Refine analyzeLuzzati coordinate error obs: 0.19 Å
Refinement stepCycle: final / Resolution: 1.5→21.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1708 0 40 221 1969
Biso mean--34.76 39.29 -
Num. residues----219
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d649SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes325HARMONIC5
X-RAY DIFFRACTIONt_it1789HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion231SEMIHARMONIC5
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_contact2305SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d1789HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg2418HARMONIC21.12
X-RAY DIFFRACTIONt_omega_torsion3.61
X-RAY DIFFRACTIONt_other_torsion16.13
LS refinement shellResolution: 1.5→1.51 Å / Rfactor Rfree error: 0 / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.3259 32 5.02 %
Rwork0.2306 605 -
all0.2348 637 -
obs--95.98 %

+
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