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- PDB-3cmt: Mechanism of homologous recombination from the RecA-ssDNA/dsDNA s... -

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Basic information

Entry
Database: PDB / ID: 3cmt
TitleMechanism of homologous recombination from the RecA-ssDNA/dsDNA structures
Components
  • DNA (5'-D(*DTP*DTP*DTP*DTP*DTP*DCP*DCP*DCP*DAP*DCP*DCP*DTP*DTP*DTP*DT)-3')
  • DNA (5'-D(P*DGP*DGP*DTP*DGP*DGP*DG)-3')
  • Protein recA
Keywordsrecombination/DNA / homologous recombination / ATP-binding / Cytoplasm / DNA damage / DNA recombination / DNA repair / DNA-binding / Nucleotide-binding / SOS response / Stress response / recombination-DNA COMPLEX
Function / homology
Function and homology information


DNA polymerase V complex / homologous recombination / recombinational repair / ATP-dependent DNA damage sensor activity / response to ionizing radiation / SOS response / ATP-dependent activity, acting on DNA / translesion synthesis / cell motility / single-stranded DNA binding ...DNA polymerase V complex / homologous recombination / recombinational repair / ATP-dependent DNA damage sensor activity / response to ionizing radiation / SOS response / ATP-dependent activity, acting on DNA / translesion synthesis / cell motility / single-stranded DNA binding / DNA-binding transcription factor binding / DNA recombination / damaged DNA binding / DNA damage response / ATP hydrolysis activity / ATP binding / cytoplasm / cytosol
Similarity search - Function
RecA protein, C-terminal domain / Rec A Protein; domain 2 / : / : / RecA C-terminal domain / DNA recombination/repair protein RecA, conserved site / DNA recombination and repair protein RecA, C-terminal / recA signature. / DNA recombination and repair protein RecA / recA bacterial DNA recombination protein ...RecA protein, C-terminal domain / Rec A Protein; domain 2 / : / : / RecA C-terminal domain / DNA recombination/repair protein RecA, conserved site / DNA recombination and repair protein RecA, C-terminal / recA signature. / DNA recombination and repair protein RecA / recA bacterial DNA recombination protein / 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. / 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 / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / TETRAFLUOROALUMINATE ION / DNA / DNA (> 10) / Protein RecA
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.15 Å
AuthorsChen, Z. / Yang, H. / Pavletich, N.P.
CitationJournal: Nature / Year: 2008
Title: Mechanism of homologous recombination from the RecA-ssDNA/dsDNA structures.
Authors: Chen, Z. / Yang, H. / Pavletich, N.P.
History
DepositionMar 24, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 20, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 26, 2017Group: Advisory / Source and taxonomy / Category: entity_src_gen / pdbx_unobs_or_zero_occ_atoms
Revision 1.3Feb 21, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_ref_seq / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_asym_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_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _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
B: DNA (5'-D(*DTP*DTP*DTP*DTP*DTP*DCP*DCP*DCP*DAP*DCP*DCP*DTP*DTP*DTP*DT)-3')
C: DNA (5'-D(P*DGP*DGP*DTP*DGP*DGP*DG)-3')
E: DNA (5'-D(*DTP*DTP*DTP*DTP*DTP*DCP*DCP*DCP*DAP*DCP*DCP*DTP*DTP*DTP*DT)-3')
F: DNA (5'-D(P*DGP*DGP*DTP*DGP*DGP*DG)-3')
A: Protein recA
D: Protein recA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)382,74036
Polymers377,1966
Non-polymers5,54530
Water00
1
B: DNA (5'-D(*DTP*DTP*DTP*DTP*DTP*DCP*DCP*DCP*DAP*DCP*DCP*DTP*DTP*DTP*DT)-3')
C: DNA (5'-D(P*DGP*DGP*DTP*DGP*DGP*DG)-3')
A: Protein recA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)191,37018
Polymers188,5983
Non-polymers2,77215
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11760 Å2
ΔGint-137.1 kcal/mol
Surface area63850 Å2
MethodPISA
2
E: DNA (5'-D(*DTP*DTP*DTP*DTP*DTP*DCP*DCP*DCP*DAP*DCP*DCP*DTP*DTP*DTP*DT)-3')
F: DNA (5'-D(P*DGP*DGP*DTP*DGP*DGP*DG)-3')
D: Protein recA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)191,37018
Polymers188,5983
Non-polymers2,77215
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11880 Å2
ΔGint-141.4 kcal/mol
Surface area63560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)159.000, 300.500, 80.100
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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DNA chain , 2 types, 4 molecules BECF

#1: DNA chain DNA (5'-D(*DTP*DTP*DTP*DTP*DTP*DCP*DCP*DCP*DAP*DCP*DCP*DTP*DTP*DTP*DT)-3')


Mass: 4451.894 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: CBHII
#2: DNA chain DNA (5'-D(P*DGP*DGP*DTP*DGP*DGP*DG)-3')


Mass: 1905.264 Da / Num. of mol.: 2 / Source method: obtained synthetically

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Protein , 1 types, 2 molecules AD

#3: Protein Protein recA / Recombinase A


Mass: 182240.656 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: cbhII / References: UniProt: P0A7G6

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Non-polymers , 3 types, 30 molecules

#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Mg
#5: Chemical
ChemComp-ALF / TETRAFLUOROALUMINATE ION


Mass: 102.975 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: AlF4
#6: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.54 Å3/Da / Density % sol: 51.51 %
Crystal growpH: 8
Details: the RecA5 fusion protein was incubated with a 1.5-fold molar excess of the primary d(T5C3AC2T4) oligonucleotide in protein buffer supplemented with 2 mM ADP, 10 mM MgCl2 and 8 mM AlF4, pH 6. ...Details: the RecA5 fusion protein was incubated with a 1.5-fold molar excess of the primary d(T5C3AC2T4) oligonucleotide in protein buffer supplemented with 2 mM ADP, 10 mM MgCl2 and 8 mM AlF4, pH 6.0, for 30 min, followed by the addition of 2-fold molar excess of the complementary d(G2TG3) oligonucleotide. The crystals grew from 50 mM Tris-Cl, 9% (w/v) PVP K15, 32% (v/v) MPD, 100 mM magnesium acetate, 10 mM DTT, pH 8.0.
Components of the solutions
IDNameCrystal-IDSol-ID
1ADP11
2MgCl211
3AlF411
4Tris-Cl11
5PVP K1511
6MPD11
7magnesium acetate11
810 mM DTT11
9Tris-Cl12
10PVP K1512
11MPD12
12magnesium acetate12
1310 mM DTT12

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C
DetectorDate: Jul 1, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 3.15→40 Å / Num. obs: 59390

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Processing

SoftwareName: REFMAC / Version: 5.3.0036 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.15→40 Å / Cor.coef. Fo:Fc: 0.92 / Cor.coef. Fo:Fc free: 0.902 / SU B: 45.573 / SU ML: 0.373 / Cross valid method: THROUGHOUT / ESU R Free: 0.521 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.243 1231 2 %RANDOM
Rwork0.217 ---
obs0.218 59390 89.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 50.72 Å2
Baniso -1Baniso -2Baniso -3
1-1.53 Å20 Å20 Å2
2---0.63 Å20 Å2
3----0.91 Å2
Refinement stepCycle: LAST / Resolution: 3.15→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms24250 732 330 0 25312
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.02225702
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.172.03434754
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.15653204
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.39225.399991
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.073154615
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.72115136
X-RAY DIFFRACTIONr_chiral_restr0.0730.23987
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0218422
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2010.211326
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3070.217338
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1250.2851
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0560.21
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.4210.296
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.5590.21
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8451.2516183
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.498225245
X-RAY DIFFRACTIONr_scbond_it1.643210759
X-RAY DIFFRACTIONr_scangle_it2.70639509
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.15→3.23 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.404 77 -
Rwork0.34 4009 -
obs--83.35 %

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