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- PDB-4a6p: RadA C-terminal ATPase domain from Pyrococcus furiosus -

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Basic information

Entry
Database: PDB / ID: 4a6p
TitleRadA C-terminal ATPase domain from Pyrococcus furiosus
ComponentsDNA REPAIR AND RECOMBINATION PROTEIN RADA
KeywordsHYDROLASE / 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)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.498 Å
AuthorsMarsh, M.E. / Ehebauer, M.T. / Scott, D. / Abell, C. / Blundell, T.L. / Hyvonen, M.
CitationJournal: FEBS Open Bio / Year: 2016
Title: ATP Half-Sites in Rada and Rad51 Recombinases Bind Nucleotides
Authors: Marsh, M.E. / Scott, D.E. / Ehebauer, M.T. / Abell, C. / Blundell, T.L. / Hyvonen, M.
History
DepositionNov 8, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 14, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 20, 2016Group: Database references
Revision 1.2Jul 27, 2016Group: Database references
Revision 1.3Dec 20, 2023Group: 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_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_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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,6052
Polymers25,5101
Non-polymers951
Water7,782432
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)60.920, 40.186, 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


Mass: 25510.150 Da / Num. of mol.: 1
Fragment: C-TERMINAL ATPASE DOMAIN, RESIDUES 108-288 AND 301-349
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PYROCOCCUS FURIOSUS (archaea) / Plasmid: PBAT / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: O74036
#2: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 432 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsC TERMINAL DOMAIN RESIDUES 108-349

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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: 41.34 % / Description: NONE
Crystal growpH: 5.8 / Details: 60 MM NA2HPO4 PH 6.0; 15% PEG 1000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795
DetectorType: ADSC CCD / Detector: CCD / Date: Apr 19, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.5→43.61 Å / Num. obs: 32321 / % possible obs: 92.4 % / Observed criterion σ(I): 3 / Redundancy: 4.8 % / Biso Wilson estimate: 7.99 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 17.4
Reflection shellResolution: 1.5→1.58 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.55 / Mean I/σ(I) obs: 3.6 / % possible all: 87.7

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1PZN

1pzn


Resolution: 1.498→26.589 Å / SU ML: 0.16 / σ(F): 1.99 / Phase error: 21.08 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2137 1623 5.1 %
Rwork0.1836 --
obs0.1852 31691 90.06 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 37.983 Å2 / ksol: 0.308 e/Å3
Displacement parametersBiso mean: 14.758 Å2
Baniso -1Baniso -2Baniso -3
1-1.3025 Å20 Å20 Å2
2--0.248 Å20 Å2
3----1.5505 Å2
Refinement stepCycle: LAST / Resolution: 1.498→26.589 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1710 0 5 432 2147
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061905
X-RAY DIFFRACTIONf_angle_d1.0262595
X-RAY DIFFRACTIONf_dihedral_angle_d15.337729
X-RAY DIFFRACTIONf_chiral_restr0.069298
X-RAY DIFFRACTIONf_plane_restr0.004344
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4982-1.54220.39671130.36192046X-RAY DIFFRACTION75
1.5422-1.5920.26291390.20722542X-RAY DIFFRACTION93
1.592-1.64890.22591340.1862604X-RAY DIFFRACTION94
1.6489-1.71490.24411220.18292561X-RAY DIFFRACTION93
1.7149-1.79290.23861350.1842585X-RAY DIFFRACTION94
1.7929-1.88750.2191380.19712560X-RAY DIFFRACTION93
1.8875-2.00570.22451200.2212174X-RAY DIFFRACTION78
2.0057-2.16050.22051420.18692335X-RAY DIFFRACTION85
2.1605-2.37780.21661080.172478X-RAY DIFFRACTION88
2.3778-2.72150.19931660.16992665X-RAY DIFFRACTION96
2.7215-3.42770.2091690.15822714X-RAY DIFFRACTION97
3.4277-26.59310.16231370.15722804X-RAY DIFFRACTION94

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