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- PDB-4d6p: RADA C-TERMINAL ATPASE DOMAIN FROM PYROCOCCUS FURIOSUS BOUND TO AMPPNP -

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Basic information

Entry
Database: PDB / ID: 4d6p
TitleRADA C-TERMINAL ATPASE DOMAIN FROM PYROCOCCUS FURIOSUS BOUND TO AMPPNP
ComponentsDNA REPAIR AND RECOMBINATION PROTEIN RADA
KeywordsHYDROLASE / RECOMBINASE / ATPASE / AMPPNP
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
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / DNA repair and recombination protein RadA
Similarity search - Component
Biological speciesPYROCOCCUS FURIOSUS (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.482 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 13, 2014Deposition site: PDBE / Processing site: PDBE
SupersessionJan 14, 2015ID: 4A74
Revision 1.0Jan 14, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 20, 2016Group: Database references
Revision 1.2Jul 27, 2016Group: Database references
Revision 1.3Dec 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.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)52,2658
Polymers51,0202
Non-polymers1,2456
Water10,773598
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A: DNA REPAIR AND RECOMBINATION PROTEIN RADA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,1334
Polymers25,5101
Non-polymers6233
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)26,1334
Polymers25,5101
Non-polymers6233
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)40.454, 87.420, 62.226
Angle α, β, γ (deg.)90.00, 91.46, 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: C-TERMINAL ATPASE DOMAIN, 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) / References: UniProt: O74036
#2: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 598 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsDELETION OF RESIDUES 1-107 AND REPLACEMENT OF RESIDUES 288- 300 WITH AN ASPARAGINE

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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: 2.17 Å3/Da / Density % sol: 43 % / 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: SLS / Beamline: X06DA / Wavelength: 0.9793
DetectorType: MARRESEARCH / Detector: CCD / Date: Jun 15, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.48→43.71 Å / Num. obs: 126096 / % possible obs: 88.1 % / Observed criterion σ(I): 2 / Redundancy: 1.92 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 8.76
Reflection shellResolution: 1.48→1.57 Å / Redundancy: 1.92 % / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 2.02 / % possible all: 89.4

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE: 1.8.4_1496)refinement
XDSdata reduction
XDSdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4A6P

4a6p


Resolution: 1.482→40.441 Å / SU ML: 0.19 / σ(F): 1.34 / Phase error: 21.98 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.239 3332 5 %
Rwork0.1903 --
obs0.1926 67222 93.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.482→40.441 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3546 0 76 598 4220
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083719
X-RAY DIFFRACTIONf_angle_d1.2135038
X-RAY DIFFRACTIONf_dihedral_angle_d14.6861398
X-RAY DIFFRACTIONf_chiral_restr0.081580
X-RAY DIFFRACTIONf_plane_restr0.005645
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4823-1.50350.33791300.27332660X-RAY DIFFRACTION94
1.5035-1.52590.26521520.20082803X-RAY DIFFRACTION100
1.5259-1.54980.24021610.18292829X-RAY DIFFRACTION100
1.5498-1.57520.22571440.17162797X-RAY DIFFRACTION100
1.5752-1.60240.2161360.17112855X-RAY DIFFRACTION100
1.6024-1.63150.24051610.16962837X-RAY DIFFRACTION100
1.6315-1.66290.23551290.16732793X-RAY DIFFRACTION100
1.6629-1.69680.21941700.16162799X-RAY DIFFRACTION100
1.6968-1.73370.21761380.15652843X-RAY DIFFRACTION100
1.7337-1.7740.23141390.15772854X-RAY DIFFRACTION100
1.774-1.81840.23891270.16162858X-RAY DIFFRACTION100
1.8184-1.86760.23141630.182794X-RAY DIFFRACTION100
1.8676-1.92250.3671770.29971456X-RAY DIFFRACTION51
1.9225-1.98460.3224970.2571880X-RAY DIFFRACTION67
1.9846-2.05550.2211620.16842818X-RAY DIFFRACTION100
2.0555-2.13780.21261600.172851X-RAY DIFFRACTION100
2.1378-2.23510.24561060.20252261X-RAY DIFFRACTION80
2.2351-2.35290.3641070.37211999X-RAY DIFFRACTION72
2.3529-2.50030.23391540.18772861X-RAY DIFFRACTION100
2.5003-2.69330.22891300.18872855X-RAY DIFFRACTION100
2.6933-2.96430.24551560.18312826X-RAY DIFFRACTION100
2.9643-3.3930.2071570.16642838X-RAY DIFFRACTION100
3.393-4.27410.24871270.17282642X-RAY DIFFRACTION92
4.2741-40.45590.18991490.15682881X-RAY DIFFRACTION99

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