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- PDB-5fot: HUMANISED MONOMERIC RADA IN COMPLEX WITH FHTU TETRAPEPTIDE -

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Basic information

Entry
Database: PDB / ID: 5fot
TitleHUMANISED MONOMERIC RADA IN COMPLEX WITH FHTU TETRAPEPTIDE
Components
  • DNA REPAIR AND RECOMBINATION PROTEIN RADA
  • FHTU 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 / 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: 1.189 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 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)26,1113
Polymers26,0162
Non-polymers951
Water6,323351
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1250 Å2
ΔGint-13.2 kcal/mol
Surface area10810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.220, 60.632, 87.431
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 FHTU PEPTIDE


Mass: 513.590 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: ACETYLATED AT THE N-TERMINUS AND AMIDATED IN THE C-TERMINUS. RESIDUE 4 IS AMINO BUTYRIC ACID, WITH TWO CARBON SIDE CHAIN
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 351 / 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: 41.4 % / 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: SLS / Beamline: X06DA / Wavelength: 0.9794
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 6, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.19→23.3 Å / Num. obs: 69123 / % possible obs: 90.8 % / Observed criterion σ(I): 2 / Redundancy: 3.22 % / Biso Wilson estimate: 13.9 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 14.46
Reflection shellResolution: 1.19→1.26 Å / Redundancy: 1.77 % / Rmerge(I) obs: 0.27 / Mean I/σ(I) obs: 2.76 / % possible all: 65.1

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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: 1.189→31.296 Å / SU ML: 0.09 / σ(F): 1.14 / Phase error: 14.06 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1567 6376 5.1 %
Rwork0.1324 --
obs0.1337 66255 94.33 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 14.6 Å2
Refinement stepCycle: LAST / Resolution: 1.189→31.296 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1792 0 5 351 2148
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0112023
X-RAY DIFFRACTIONf_angle_d1.3742754
X-RAY DIFFRACTIONf_dihedral_angle_d12.968786
X-RAY DIFFRACTIONf_chiral_restr0.075306
X-RAY DIFFRACTIONf_plane_restr0.006369
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.1891-1.20260.26341580.22132421X-RAY DIFFRACTION59
1.2026-1.21670.23291710.21112936X-RAY DIFFRACTION69
1.2167-1.23160.20951610.19753113X-RAY DIFFRACTION75
1.2316-1.24720.20641850.19493391X-RAY DIFFRACTION81
1.2472-1.26360.21061820.18433565X-RAY DIFFRACTION84
1.2636-1.28090.22761710.17463664X-RAY DIFFRACTION88
1.2809-1.29920.17142370.16823897X-RAY DIFFRACTION92
1.2992-1.31860.19852160.15624005X-RAY DIFFRACTION95
1.3186-1.33920.15662090.14764091X-RAY DIFFRACTION98
1.3392-1.36110.16032480.14284093X-RAY DIFFRACTION99
1.3611-1.38460.16182270.13294187X-RAY DIFFRACTION100
1.3846-1.40980.17192200.1224202X-RAY DIFFRACTION100
1.4098-1.43690.16862280.12024227X-RAY DIFFRACTION99
1.4369-1.46620.15521990.11744135X-RAY DIFFRACTION100
1.4662-1.49810.16622260.11384198X-RAY DIFFRACTION100
1.4981-1.5330.14242090.11184193X-RAY DIFFRACTION100
1.533-1.57130.14271920.10914193X-RAY DIFFRACTION100
1.5713-1.61380.1462250.10594241X-RAY DIFFRACTION100
1.6138-1.66130.12782300.11464199X-RAY DIFFRACTION100
1.6613-1.71490.16311980.11364206X-RAY DIFFRACTION100
1.7149-1.77620.16182410.11894191X-RAY DIFFRACTION100
1.7762-1.84730.16712210.12524163X-RAY DIFFRACTION100
1.8473-1.93130.19332070.12144211X-RAY DIFFRACTION100
1.9313-2.03310.14171960.12424219X-RAY DIFFRACTION100
2.0331-2.16050.14632720.12324101X-RAY DIFFRACTION99
2.1605-2.32730.16062300.12354189X-RAY DIFFRACTION99
2.3273-2.56140.15382130.1274159X-RAY DIFFRACTION99
2.5614-2.93180.12782460.13254184X-RAY DIFFRACTION100
2.9318-3.69280.13952390.13144175X-RAY DIFFRACTION100
3.6928-31.30640.14612190.14334132X-RAY DIFFRACTION98

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