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- PDB-2i1q: RadA Recombinase in complex with Calcium -

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Basic information

Entry
Database: PDB / ID: 2i1q
TitleRadA Recombinase in complex with Calcium
ComponentsDNA repair and recombination protein radA
KeywordsRECOMBINATION / ATPASE / RECOMBINASE / ATP COMPLEX / Calcium stimulation / RecA / Rad51 / DMC1 / RadA
Function / homology
Function and homology information


ATP-dependent DNA damage sensor activity / DNA recombination / damaged DNA binding / DNA repair / ATP hydrolysis activity / ATP binding / identical protein 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 / 5' to 3' exonuclease, C-terminal subdomain / DNA polymerase; domain 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 / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / DNA repair and recombination protein RadA
Similarity search - Component
Biological speciesMethanococcus voltae (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsQian, X. / He, Y. / Ma, X. / Fodje, M.N. / Grochulski, P. / Luo, Y.
CitationJournal: J.Biol.Chem. / Year: 2006
Title: Calcium Stiffens Archaeal Rad51 Recombinase from Methanococcus voltae for Homologous Recombination.
Authors: Qian, X. / He, Y. / Ma, X. / Fodje, M.N. / Grochulski, P. / Luo, Y.
History
DepositionAug 14, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 24, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_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.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _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.ptnr1_symmetry / _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_conn.ptnr2_symmetry / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA repair and recombination protein radA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,8737
Polymers35,1991
Non-polymers6746
Water2,684149
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)84.200, 84.200, 104.700
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

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Protein , 1 types, 1 molecules A

#1: Protein DNA repair and recombination protein radA


Mass: 35198.930 Da / Num. of mol.: 1 / Mutation: S2G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanococcus voltae (archaea) / Gene: RADA / Plasmid: PET28B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CODONPLUS-RIL / References: UniProt: O73948

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Non-polymers , 5 types, 155 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 149 / 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: 3.04 Å3/Da / Density % sol: 59.58 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 6% PEG 3350, 0.05M Tris-HCl, 0.005M MgCl2, 0.025M CaCl2, 0.002M ANP, pH 7.40, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 1.3303 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 3, 2004 / Details: DOUBLE CRYSTAL
RadiationMonochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.3303 Å / Relative weight: 1
ReflectionResolution: 1.9→40 Å / Num. all: 31896 / Num. obs: 31855 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 22.2 % / Rmerge(I) obs: 0.062 / Rsym value: 0.062 / Net I/σ(I): 42.4
Reflection shellResolution: 1.9→2.09 Å / Redundancy: 22 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 8.7 / Num. unique all: 5933 / Rsym value: 0.42 / % possible all: 99.4

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Processing

Software
NameVersionClassification
AMoREphasing
CNS1refinement
MAR345345DTBdata collection
XDSdata reduction
XDSdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1XU4

1xu4


Resolution: 1.9→20 Å / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: CNS REFINEMENT
RfactorNum. reflection% reflectionSelection details
Rfree0.211 1593 -RANDOM
Rwork0.191 ---
all0.191 31896 --
obs0.191 31855 99.9 %-
Refinement stepCycle: LAST / Resolution: 1.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2385 0 36 149 2570
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.18
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1PROTEIN_REP.PARAM
X-RAY DIFFRACTION2ANP_XPLOR.PARAM
X-RAY DIFFRACTION3WATER_REP.PARAM
X-RAY DIFFRACTION4ION.PARAM
X-RAY DIFFRACTION5CIS_PEPTIDE.PARAM

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