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- PDB-5fox: HUMANISED MONOMERIC RADA IN COMPLEX WITH FHAA TETRAPEPTIDE -

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Basic information

Entry
Database: PDB / ID: 5fox
TitleHUMANISED MONOMERIC RADA IN COMPLEX WITH FHAA TETRAPEPTIDE
Components
  • DNA REPAIR AND RECOMBINATION PROTEIN RADA
  • FHAA PEPTIDE
KeywordsHYDROLASE / RADA / FXXA MOTIF / RECOMBINASE
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 / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / DNA repair and recombination protein RadA
Similarity search - Component
Biological speciesPYROCOCCUS FURIOSUS (archaea)
HOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsScott, D.E. / Marsh, M. / Blundell, T.L. / Abell, C. / Hyvonen, M.
CitationJournal: FEBS Lett. / Year: 2016
Title: Structure Activity Relationship of the Peptide Binding Motif Mediating the Rad51:Brca2 Protein-Protein Interaction.
Authors: Scott, D.E. / Marsh, M. / Blundell, T.L. / Abell, C. / Hyvonen, M.
History
DepositionNov 26, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 30, 2016Provider: repository / Type: Initial release
Revision 1.1May 11, 2016Group: Database references
Revision 1.2Jun 27, 2018Group: Data collection / Database references / Category: struct_ref_seq_dif / Item: _struct_ref_seq_dif.details
Revision 2.0Oct 23, 2019Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Other
Category: atom_site / pdbx_database_status / struct_conn
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag
Revision 2.1Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.2Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA REPAIR AND RECOMBINATION PROTEIN RADA
C: FHAA PEPTIDE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,1594
Polymers25,9722
Non-polymers1872
Water5,386299
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1430 Å2
ΔGint-14 kcal/mol
Surface area10310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.841, 117.623, 40.248
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein DNA REPAIR AND RECOMBINATION PROTEIN RADA / RADA RECOMBINASE


Mass: 25502.150 Da / Num. of mol.: 1 / Fragment: ATPASE, UNP RESIDUES 108-349 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PYROCOCCUS FURIOSUS (archaea) / Plasmid: PBAT4 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PUBS520
References: UniProt: O74036, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement
#2: Protein/peptide FHAA PEPTIDE


Mass: 469.537 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: ACETYLATED AT THE N-TERMINUS AND AMIDATED IN THE C-TERMINUS
Source: (synth.) HOMO SAPIENS (human)
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


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


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 299 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsMUTATIONS I169M, Y201A, V202Y, K221M AND REPLACEMENT OF LOOP 287-300 BY AN N.

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.18 Å3/Da / Density % sol: 44 % / Description: NONE
Crystal growpH: 6 / Details: 8% PEG-1000, 100 MM NAK PHOSPHATE, PH 6.2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795
DetectorType: MARREAEARCH / Detector: CCD / Date: Apr 18, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.3→36.64 Å / Num. obs: 55533 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Redundancy: 6.69 % / Biso Wilson estimate: 16.515 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 15.6
Reflection shellResolution: 1.3→1.38 Å / Redundancy: 6.22 % / Rmerge(I) obs: 0.8 / Mean I/σ(I) obs: 2.44 / % possible all: 99.7

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XDSdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4B3B

4b3b


Resolution: 1.3→30.527 Å / SU ML: 0.12 / σ(F): 1.99 / Phase error: 16.55 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1819 2868 5.2 %
Rwork0.1566 --
obs0.1579 55532 99.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 15.72 Å2
Refinement stepCycle: LAST / Resolution: 1.3→30.527 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1759 0 11 299 2069
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062022
X-RAY DIFFRACTIONf_angle_d1.1392754
X-RAY DIFFRACTIONf_dihedral_angle_d14.311777
X-RAY DIFFRACTIONf_chiral_restr0.067304
X-RAY DIFFRACTIONf_plane_restr0.005369
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3001-1.32250.26051510.22452549X-RAY DIFFRACTION99
1.3225-1.34650.21361360.21342618X-RAY DIFFRACTION100
1.3465-1.37240.22641430.18872605X-RAY DIFFRACTION100
1.3724-1.40040.22481360.18032599X-RAY DIFFRACTION100
1.4004-1.43090.20221500.18072604X-RAY DIFFRACTION100
1.4309-1.46420.21141290.1782589X-RAY DIFFRACTION100
1.4642-1.50080.20511480.16142613X-RAY DIFFRACTION100
1.5008-1.54140.17891350.14672614X-RAY DIFFRACTION100
1.5414-1.58670.19871260.14422607X-RAY DIFFRACTION100
1.5867-1.63790.1951440.14722635X-RAY DIFFRACTION100
1.6379-1.69650.20011310.14772611X-RAY DIFFRACTION100
1.6965-1.76440.19611620.14912625X-RAY DIFFRACTION100
1.7644-1.84470.18731680.14212591X-RAY DIFFRACTION100
1.8447-1.94190.16431560.15572618X-RAY DIFFRACTION100
1.9419-2.06360.15131410.13892647X-RAY DIFFRACTION100
2.0636-2.22280.18821230.1422665X-RAY DIFFRACTION100
2.2228-2.44640.16211480.14562625X-RAY DIFFRACTION99
2.4464-2.80020.18891490.15592686X-RAY DIFFRACTION100
2.8002-3.52720.1571300.15712729X-RAY DIFFRACTION100
3.5272-30.53520.17121620.15922834X-RAY DIFFRACTION99

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