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- PDB-5fou: HUMANISED MONOMERIC RADA IN COMPLEX WITH FHPA TETRAPEPTIDE -

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Basic information

Entry
Database: PDB / ID: 5fou
TitleHUMANISED MONOMERIC RADA IN COMPLEX WITH FHPA TETRAPEPTIDE
Components
  • DNA REPAIR AND RECOMBINATION PROTEIN RADA
  • FHPA PEPTIDE
KeywordsHYDROLASE / 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 / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 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: 1.5 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 1.2Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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: FHPA PEPTIDE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,1884
Polymers25,9982
Non-polymers1902
Water7,386410
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1480 Å2
ΔGint-22.9 kcal/mol
Surface area11120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.263, 60.571, 87.927
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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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 FHPA PEPTIDE


Mass: 495.574 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 / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 410 / Source method: isolated from a natural source / Formula: H2O
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: 2.11 Å3/Da / Density % sol: 41.8 % / Description: NONE
Crystal growpH: 6.2 / 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: I04 / Wavelength: 0.97952
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 16, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97952 Å / Relative weight: 1
ReflectionResolution: 1.5→43.96 Å / Num. obs: 35168 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Redundancy: 6.98 % / Biso Wilson estimate: 18.3 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 13.96
Reflection shellResolution: 1.5→1.59 Å / Redundancy: 6.65 % / Rmerge(I) obs: 0.86 / Mean I/σ(I) obs: 2.22 / % possible all: 99.3

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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: 1.5→43.964 Å / SU ML: 0.15 / σ(F): 1.99 / Phase error: 17.71 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1924 1768 5 %
Rwork0.1642 --
obs0.1656 35160 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 15.7 Å2
Refinement stepCycle: LAST / Resolution: 1.5→43.964 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1801 0 10 410 2221
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071919
X-RAY DIFFRACTIONf_angle_d0.9582604
X-RAY DIFFRACTIONf_dihedral_angle_d12.368727
X-RAY DIFFRACTIONf_chiral_restr0.046293
X-RAY DIFFRACTIONf_plane_restr0.004343
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.54060.28541300.24512511X-RAY DIFFRACTION99
1.5406-1.58590.22951270.2242515X-RAY DIFFRACTION100
1.5859-1.63710.25731360.20432530X-RAY DIFFRACTION100
1.6371-1.69560.251230.19572557X-RAY DIFFRACTION100
1.6956-1.76350.19521320.17762526X-RAY DIFFRACTION100
1.7635-1.84370.20731290.17272569X-RAY DIFFRACTION100
1.8437-1.9410.21211270.16562561X-RAY DIFFRACTION100
1.941-2.06260.18921330.15932538X-RAY DIFFRACTION100
2.0626-2.22180.17191570.14532545X-RAY DIFFRACTION100
2.2218-2.44540.17291420.14812575X-RAY DIFFRACTION100
2.4454-2.79920.19511280.16012600X-RAY DIFFRACTION100
2.7992-3.52640.17261610.14962603X-RAY DIFFRACTION100
3.5264-43.98240.17381430.14852762X-RAY DIFFRACTION100

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