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- PDB-4uqo: RADA C-TERMINAL ATPASE DOMAIN FROM PYROCOCCUS FURIOSUS BOUND TO ADP -

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Basic information

Entry
Database: PDB / ID: 4uqo
TitleRADA C-TERMINAL ATPASE DOMAIN FROM PYROCOCCUS FURIOSUS BOUND TO ADP
ComponentsDNA REPAIR AND RECOMBINATION PROTEIN RADA
KeywordsHYDROLASE / RADA / RECOMBINASE / ATPASE / ADP
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
ADENOSINE-5'-DIPHOSPHATE / DNA repair and recombination protein RadA
Similarity search - Component
Biological speciesPYROCOCCUS FURIOSUS (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.88 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
DepositionJun 24, 2014Deposition site: PDBE / Processing site: PDBE
SupersessionJan 14, 2015ID: 4A7O
Revision 1.0Jan 14, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 20, 2016Group: Database references
Revision 1.2Jul 27, 2016Group: Database references
Revision 1.3Jan 10, 2024Group: 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.ptnr1_label_seq_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.ptnr3_label_seq_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

Downloads & links

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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)51,9929
Polymers51,0202
Non-polymers9727
Water8,935496
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A: DNA REPAIR AND RECOMBINATION PROTEIN RADA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,9854
Polymers25,5101
Non-polymers4743
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)26,0085
Polymers25,5101
Non-polymers4974
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)40.308, 87.130, 62.322
Angle α, β, γ (deg.)90.00, 90.55, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-1, 0.00441, -0.000132), (-0.00441, -1, 0.005209), (-0.000109, 0.00521, 1)
Vector: 20.07, 23.98, -31.19)

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Components

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


Mass: 25510.150 Da / Num. of mol.: 2 / Fragment: C-TERMINAL ATPASE DOMAIN, 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) / References: UniProt: O74036
#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 496 / 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: 2.15 Å3/Da / Density % sol: 43 % / Description: NONE
Crystal growpH: 5.8 / Details: 60 MM NAPHOSPHATE PH 5.8, 15% PEG1000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9728
DetectorType: ADSC CCD / Detector: 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: 1.88→43.56 Å / Num. obs: 34773 / % possible obs: 99.1 % / Observed criterion σ(I): 2 / Redundancy: 3.51 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 10.44
Reflection shellResolution: 1.88→1.99 Å / Redundancy: 3.47 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 2.61 / % possible all: 96.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0071refinement
XDSdata reduction
XDSdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4A6P

4a6p


Resolution: 1.88→62.32 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.922 / SU B: 4.529 / SU ML: 0.128 / Cross valid method: THROUGHOUT / ESU R: 0.162 / ESU R Free: 0.156 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES A287-A306 AND B286-B304 ARE DISORDERED.
RfactorNum. reflection% reflectionSelection details
Rfree0.2314 1719 4.9 %RANDOM
Rwork0.17124 ---
obs0.17416 33051 99.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.423 Å2
Baniso -1Baniso -2Baniso -3
1-1.85 Å20 Å2-0.34 Å2
2---2.06 Å20 Å2
3---0.21 Å2
Refinement stepCycle: LAST / Resolution: 1.88→62.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3472 0 59 496 4027
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0193623
X-RAY DIFFRACTIONr_bond_other_d0.0040.023573
X-RAY DIFFRACTIONr_angle_refined_deg1.7921.9894906
X-RAY DIFFRACTIONr_angle_other_deg1.08738196
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1845449
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.12123.78164
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.90915652
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1711531
X-RAY DIFFRACTIONr_chiral_restr0.1070.2563
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.024066
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02823
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.8981.9371795
X-RAY DIFFRACTIONr_mcbond_other1.8951.9371794
X-RAY DIFFRACTIONr_mcangle_it2.9932.8882243
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.6512.3211828
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.88→1.929 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.298 116 -
Rwork0.298 2307 -
obs--93.73 %

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