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- PDB-5fos: HUMANISED MONOMERIC RADA IN COMPLEX WITH OLIGOMERISATION PEPTIDE -

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Basic information

Entry
Database: PDB / ID: 5fos
TitleHUMANISED MONOMERIC RADA IN COMPLEX WITH OLIGOMERISATION PEPTIDE
Components(DNA REPAIR AND RECOMBINATION PROTEIN RADA) x 2
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)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å
AuthorsSharpe, T. / Moschetti, T. / Fischer, G. / Marsh, M. / Blundell, T.L. / Abell, C. / Hyvonen, M.
CitationJournal: J.Mol.Biol. / Year: 2016
Title: Engineering Archeal Surrogate Systems for the Development of Protein-Protein Interaction Inhibitors against Human RAD51.
Authors: Moschetti, T. / Sharpe, T. / Fischer, G. / Marsh, M.E. / Ng, H.K. / Morgan, M. / Scott, D.E. / Blundell, T.L. / R Venkitaraman, A. / Skidmore, J. / Abell, C. / Hyvonen, M.
History
DepositionNov 26, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 19, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 30, 2016Group: Database references
Revision 1.2Mar 29, 2023Group: Database references / Derived calculations / Other
Category: citation / citation_author ...citation / citation_author / database_2 / pdbx_database_status / struct_conn / struct_site
Item: _citation.journal_id_ISSN / _citation.page_last ..._citation.journal_id_ISSN / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation_author.name / _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
Revision 1.3Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.4Nov 6, 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: DNA REPAIR AND RECOMBINATION PROTEIN RADA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,8817
Polymers27,4172
Non-polymers4635
Water5,224290
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2120 Å2
ΔGint-16.4 kcal/mol
Surface area11720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.790, 61.780, 87.220
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 DNA REPAIR AND RECOMBINATION PROTEIN RADA / RADA RECOMBINASE


Mass: 1915.245 Da / Num. of mol.: 1 / Fragment: OLIGOMERISATION PEPTIDE, UNP RESIDUES 93-108 / Source method: obtained synthetically / Source: (synth.) PYROCOCCUS FURIOSUS (archaea)
References: UniProt: O74036, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement
#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.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 290 / 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. MUTATIONS I169M, ...MUTATIONS I169M, Y201A, V202Y, K221M AND REPLACEMENT OF LOOP 287-300 BY AN N. MUTATIONS 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: 2.16 Å3/Da / Density % sol: 43.2 % / 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: I03 / Wavelength: 0.97
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 31, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.35→36.95 Å / Num. obs: 47394 / % possible obs: 96.3 % / Observed criterion σ(I): 2 / Redundancy: 4.9 % / Biso Wilson estimate: 18.5 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 16.33
Reflection shellResolution: 1.35→1.43 Å / Redundancy: 4.77 % / Rmerge(I) obs: 0.55 / Mean I/σ(I) obs: 2.65 / % possible all: 98.6

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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 1PZN

1pzn


Resolution: 1.35→36.949 Å / SU ML: 0.12 / σ(F): 1.99 / Phase error: 15.99 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1815 2399 5.1 %
Rwork0.1414 --
obs0.1434 47391 96.27 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 18.4 Å2
Refinement stepCycle: LAST / Resolution: 1.35→36.949 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1875 0 29 290 2194
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091978
X-RAY DIFFRACTIONf_angle_d1.2992668
X-RAY DIFFRACTIONf_dihedral_angle_d14.033751
X-RAY DIFFRACTIONf_chiral_restr0.076301
X-RAY DIFFRACTIONf_plane_restr0.007346
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3498-1.37740.26031390.19542662X-RAY DIFFRACTION98
1.3774-1.40730.22291420.18322679X-RAY DIFFRACTION99
1.4073-1.44010.2141450.16782665X-RAY DIFFRACTION99
1.4401-1.47610.24741280.14982683X-RAY DIFFRACTION98
1.4761-1.5160.19981470.14112663X-RAY DIFFRACTION99
1.516-1.56060.17431460.12952661X-RAY DIFFRACTION98
1.5606-1.6110.20031290.12372674X-RAY DIFFRACTION98
1.611-1.66850.17691330.12742669X-RAY DIFFRACTION97
1.6685-1.73530.16431670.1252623X-RAY DIFFRACTION98
1.7353-1.81430.19041500.1222647X-RAY DIFFRACTION97
1.8143-1.910.16971330.12762651X-RAY DIFFRACTION97
1.91-2.02960.15821400.1262622X-RAY DIFFRACTION96
2.0296-2.18630.16661450.12552621X-RAY DIFFRACTION95
2.1863-2.40630.15311370.12552641X-RAY DIFFRACTION95
2.4063-2.75440.16961430.14442602X-RAY DIFFRACTION94
2.7544-3.46990.20481400.15072586X-RAY DIFFRACTION92
3.4699-36.96290.17411350.15592643X-RAY DIFFRACTION89

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