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- PDB-1pzn: Rad51 (RadA) -

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Basic information

Entry
Database: PDB / ID: 1pzn
TitleRad51 (RadA)
ComponentsDNA repair and recombination protein rad51
KeywordsRECOMBINATION / HEPTAMERIC RING / HEPTAMER / RING / OLIGOMER / RAD51 POLYMERIZATION MOTIF / HELIX-HAIRPIN-HELIX / DNA REPAIR / DNA RECOMBINATION / ATPASE / HOMOLOGOUS RECOMBINATION
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 / 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
IMIDAZOLE / DNA repair and recombination protein RadA
Similarity search - Component
Biological speciesPyrococcus furiosus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.85 Å
AuthorsShin, D.S. / Tainer, J.A.
CitationJournal: Embo J. / Year: 2003
Title: Full-length archaeal Rad51 structure and mutants: Mechanisms for RAD51 assembly and control by BRCA2
Authors: Shin, D.S. / Pellegrini, L. / Daniels, D.S. / Yelent, B. / Craig, L. / Bates, D. / Yu, D.S. / Shivji, M.K. / Hitomi, C. / Arvai, A.S. / Volkmann, N. / Tsuruta, H. / Blundell, T.L. / ...Authors: Shin, D.S. / Pellegrini, L. / Daniels, D.S. / Yelent, B. / Craig, L. / Bates, D. / Yu, D.S. / Shivji, M.K. / Hitomi, C. / Arvai, A.S. / Volkmann, N. / Tsuruta, H. / Blundell, T.L. / Venkitaraman, A.R. / Tainer, J.A.
History
DepositionJul 12, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 9, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance

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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 rad51
B: DNA repair and recombination protein rad51
C: DNA repair and recombination protein rad51
D: DNA repair and recombination protein rad51
E: DNA repair and recombination protein rad51
F: DNA repair and recombination protein rad51
G: DNA repair and recombination protein rad51
hetero molecules


Theoretical massNumber of molelcules
Total (without water)273,10036
Polymers270,5047
Non-polymers2,59629
Water1,20767
1
A: DNA repair and recombination protein rad51
B: DNA repair and recombination protein rad51
C: DNA repair and recombination protein rad51
D: DNA repair and recombination protein rad51
E: DNA repair and recombination protein rad51
F: DNA repair and recombination protein rad51
G: DNA repair and recombination protein rad51
hetero molecules

A: DNA repair and recombination protein rad51
B: DNA repair and recombination protein rad51
C: DNA repair and recombination protein rad51
D: DNA repair and recombination protein rad51
E: DNA repair and recombination protein rad51
F: DNA repair and recombination protein rad51
G: DNA repair and recombination protein rad51
hetero molecules


Theoretical massNumber of molelcules
Total (without water)546,20072
Polymers541,00814
Non-polymers5,19158
Water25214
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_353-x-2,y,-z-3/21
2


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area23830 Å2
ΔGint-227 kcal/mol
Surface area65900 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)144.163, 193.124, 176.930
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Cell settingorthorhombic
Space group name H-MC2221
DetailsThe second part of the biological assembly is generated by the two fold axis: -x, y, 1/2-z

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Components

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Protein , 1 types, 7 molecules ABCDEFG

#1: Protein
DNA repair and recombination protein rad51 / Rad51 / RadA / recombinase radA


Mass: 38643.453 Da / Num. of mol.: 7
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus (archaea) / Production host: Escherichia coli (E. coli) / References: UniProt: O74036

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Non-polymers , 5 types, 96 molecules

#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-IMD / IMIDAZOLE / Imidazole


Mass: 69.085 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C3H5N2
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 67 / 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: 2

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Sample preparation

CrystalDensity Matthews: 3.18 Å3/Da / Density % sol: 61 %
Crystal grow
*PLUS
Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
10.2 mg/mlprotein1drop
21 mMATP1drop
320 mM1dropMgCl2

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Data collection

Diffraction
IDCrystal-ID
11
21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSSRL BL9-210.979029
SYNCHROTRONSSRL BL9-220.979126, 0.911620, 0.979413
Detector
TypeIDDetectorDate
ADSC1CCDApr 7, 2002
ADSC2CCDApr 6, 2002
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9790291
20.9791261
30.911621
40.9794131
ReflectionResolution: 2.85→40 Å / Num. all: 106150 / Num. obs: 106150 / % possible obs: 97.1 % / Biso Wilson estimate: 78 Å2 / Rsym value: 0.094 / Net I/σ(I): 20.3
Reflection shellResolution: 2.85→2.95 Å / % possible obs: 89.3 % / Mean I/σ(I) obs: 3.2198 / Rsym value: 0.37
Reflection
*PLUS
Num. obs: 462283 / Rmerge(I) obs: 0.094
Reflection shell
*PLUS
Num. unique obs: 57867 / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 3.2

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
CNS1.1refinement
RefinementMethod to determine structure: MAD / Resolution: 2.85→39.12 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 5646125.88 / Data cutoff low absF: 0 / Isotropic thermal model: GROUP / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.307 5206 4.9 %RANDOM
Rwork0.257 ---
all-106150 --
obs-106150 95.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 56.162 Å2 / ksol: 0.318797 e/Å3
Displacement parametersBiso mean: 79.8 Å2
Baniso -1Baniso -2Baniso -3
1-42 Å20 Å20 Å2
2---30.42 Å20 Å2
3----11.58 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.55 Å0.47 Å
Luzzati d res low-5 Å
Luzzati sigma a0.65 Å0.68 Å
Refinement stepCycle: LAST / Resolution: 2.85→39.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13587 0 166 67 13820
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.3
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.8
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.85→3.03 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.394 793 4.8 %
Rwork0.386 15762 -
obs-16555 89.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2LIG.PARWATER.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMLIG.TOP
X-RAY DIFFRACTION4CIS_PEPTIDE.PARAMION.TOP
Refinement
*PLUS
Lowest resolution: 40 Å / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0085
X-RAY DIFFRACTIONc_angle_deg1.39
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.3
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.8

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