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- PDB-5fpk: MONOMERIC RADA IN COMPLEX WITH FATA TETRAPEPTIDE -

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Basic information

Entry
Database: PDB / ID: 5fpk
TitleMONOMERIC RADA IN COMPLEX WITH FATA TETRAPEPTIDE
Components
  • DNA REPAIR AND RECOMBINATION PROTEIN RADA
  • FHTG 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: 1.343 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
DepositionDec 1, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 30, 2016Provider: repository / Type: Initial release
Revision 1.1May 18, 2016Group: Database references
Revision 1.2Oct 23, 2019Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: pdbx_database_status / struct_conn / struct_ref_seq_dif
Item: _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.3Jan 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 1.4Nov 20, 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)26,0383
Polymers25,9432
Non-polymers951
Water7,837435
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1230 Å2
ΔGint-13.5 kcal/mol
Surface area10730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.302, 60.578, 87.447
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


Mass: 25510.150 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
#2: Protein/peptide FHTG PEPTIDE


Mass: 432.494 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 435 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsMUTATION R288N AND DELETION OF LOOP 289-300.

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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: 2.1 Å3/Da / Density % sol: 41.5 % / 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: ESRF / Beamline: ID14-4 / Wavelength: 0.9795
DetectorType: MARRESEARCH / 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: 1.34→49.8 Å / Num. obs: 47749 / % possible obs: 98.3 % / Observed criterion σ(I): 2 / Redundancy: 6.98 % / Biso Wilson estimate: 16.2 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 22.41
Reflection shellResolution: 1.34→1.42 Å / Redundancy: 6.24 % / Rmerge(I) obs: 0.61 / Mean I/σ(I) obs: 2.98 / % possible all: 92.3

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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: 1.343→43.723 Å / SU ML: 0.13 / σ(F): 1.36 / Phase error: 14.76 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1637 2377 5 %
Rwork0.123 --
obs0.1251 47745 98.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 14.9 Å2
Refinement stepCycle: LAST / Resolution: 1.343→43.723 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1804 0 5 435 2244
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091925
X-RAY DIFFRACTIONf_angle_d1.0332617
X-RAY DIFFRACTIONf_dihedral_angle_d24.181738
X-RAY DIFFRACTIONf_chiral_restr0.077301
X-RAY DIFFRACTIONf_plane_restr0.006344
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3427-1.37010.30721210.22212239X-RAY DIFFRACTION84
1.3701-1.39990.2321300.18042578X-RAY DIFFRACTION96
1.3999-1.43250.19691290.1482633X-RAY DIFFRACTION99
1.4325-1.46830.20531270.13222648X-RAY DIFFRACTION99
1.4683-1.5080.18071360.12082655X-RAY DIFFRACTION98
1.508-1.55240.17081560.11312659X-RAY DIFFRACTION99
1.5524-1.60250.17661070.11672691X-RAY DIFFRACTION100
1.6025-1.65980.18021430.11372657X-RAY DIFFRACTION99
1.6598-1.72620.15551460.10862684X-RAY DIFFRACTION99
1.7262-1.80480.17851520.10832671X-RAY DIFFRACTION100
1.8048-1.90.14331270.11172718X-RAY DIFFRACTION100
1.9-2.0190.15731070.11322747X-RAY DIFFRACTION99
2.019-2.17490.16541640.10852666X-RAY DIFFRACTION100
2.1749-2.39370.14371710.1082700X-RAY DIFFRACTION100
2.3937-2.74010.14121590.11792746X-RAY DIFFRACTION100
2.7401-3.4520.14881420.11942786X-RAY DIFFRACTION100
3.452-43.74670.16011600.13982890X-RAY DIFFRACTION99

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