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- PDB-4a6x: RadA C-terminal ATPase domain from Pyrococcus furiosus bound to ATP -

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Basic information

Entry
Database: PDB / ID: 4a6x
TitleRadA C-terminal ATPase domain from Pyrococcus furiosus bound to ATP
ComponentsDNA REPAIR AND RECOMBINATION PROTEIN RADA
KeywordsHYDROLASE / RECOMBINASE
Function / homology
Function and homology information


DNA recombinase assembly / mitotic recombination / DNA strand invasion / DNA strand exchange activity / ATP-dependent DNA damage sensor activity / single-stranded DNA binding / double-stranded DNA binding / damaged DNA binding / 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
ADENOSINE-5'-TRIPHOSPHATE / DNA repair and recombination protein RadA
Similarity search - Component
Biological speciesPYROCOCCUS FURIOSUS (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.548 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 10, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 21, 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 / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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
B: DNA REPAIR AND RECOMBINATION PROTEIN RADA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,0836
Polymers51,0202
Non-polymers1,0634
Water11,295627
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A: DNA REPAIR AND RECOMBINATION PROTEIN RADA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,0423
Polymers25,5101
Non-polymers5312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: DNA REPAIR AND RECOMBINATION PROTEIN RADA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,0423
Polymers25,5101
Non-polymers5312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)40.320, 87.350, 61.880
Angle α, β, γ (deg.)90.00, 91.23, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein DNA REPAIR AND RECOMBINATION PROTEIN RADA / RADA


Mass: 25510.150 Da / Num. of mol.: 2 / Fragment: RADA C-TERMINAL ATPASE DOMAIN, RESIDUES 108-349
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-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 627 / Source method: isolated from a natural source / Formula: H2O

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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: 2.14 Å3/Da / Density % sol: 42.52 % / Description: NONE
Crystal growpH: 5.8 / Details: 60MM NA2HPO4 PH 6.0; 15% PEG1000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9728
DetectorDetector: CCD / Date: Dec 10, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9728 Å / Relative weight: 1
ReflectionResolution: 1.55→43.67 Å / Num. obs: 59656 / % possible obs: 95.7 % / Observed criterion σ(I): 3 / Redundancy: 3.7 % / Biso Wilson estimate: 10.42 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 11.5
Reflection shellResolution: 1.55→1.63 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.65 / Mean I/σ(I) obs: 1.9 / % possible all: 93.8

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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 CODE ENTRY 4A6P

4a6p


Resolution: 1.548→43.675 Å / SU ML: 0.19 / σ(F): 1.99 / Phase error: 23.29 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2349 2899 4.9 %
Rwork0.1961 --
obs0.1979 59636 95.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 30.427 Å2 / ksol: 0.343 e/Å3
Displacement parametersBiso mean: 15.04 Å2
Baniso -1Baniso -2Baniso -3
1-3.8374 Å20 Å2-1.5125 Å2
2---4.9577 Å20 Å2
3---1.1203 Å2
Refinement stepCycle: LAST / Resolution: 1.548→43.675 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3462 0 64 627 4153
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063752
X-RAY DIFFRACTIONf_angle_d1.1155096
X-RAY DIFFRACTIONf_dihedral_angle_d17.7671436
X-RAY DIFFRACTIONf_chiral_restr0.07574
X-RAY DIFFRACTIONf_plane_restr0.004663
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5477-1.57310.28231290.2492585X-RAY DIFFRACTION93
1.5731-1.60020.29431450.24722632X-RAY DIFFRACTION94
1.6002-1.62930.28091330.23922669X-RAY DIFFRACTION94
1.6293-1.66070.30591270.22382661X-RAY DIFFRACTION95
1.6607-1.69450.28111260.21812648X-RAY DIFFRACTION94
1.6945-1.73140.2561360.21822672X-RAY DIFFRACTION95
1.7314-1.77170.30131460.20442670X-RAY DIFFRACTION94
1.7717-1.8160.2271510.20212691X-RAY DIFFRACTION95
1.816-1.86510.27281500.19662640X-RAY DIFFRACTION95
1.8651-1.920.27441310.2012704X-RAY DIFFRACTION95
1.92-1.98190.25191360.18982704X-RAY DIFFRACTION96
1.9819-2.05280.21311740.18162681X-RAY DIFFRACTION96
2.0528-2.1350.24881300.18442727X-RAY DIFFRACTION95
2.135-2.23210.23281270.18412707X-RAY DIFFRACTION96
2.2321-2.34980.22451220.18832723X-RAY DIFFRACTION97
2.3498-2.4970.26981470.19512746X-RAY DIFFRACTION97
2.497-2.68980.24491210.19582754X-RAY DIFFRACTION97
2.6898-2.96040.21161480.20362758X-RAY DIFFRACTION98
2.9604-3.38860.19881320.18312759X-RAY DIFFRACTION97
3.3886-4.26880.18831280.16792802X-RAY DIFFRACTION98
4.2688-43.69240.19541600.19032804X-RAY DIFFRACTION97

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