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

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Basic information

Entry
Database: PDB / ID: 3cmv
TitleMechanism of homologous recombination from the RecA-ssDNA/dsDNA structures
ComponentsProtein recA
KeywordsRECOMBINATION / homologous recombination
Function / homology
Function and homology information


DNA polymerase V complex / homologous recombination / recombinational repair / SOS response / ATP-dependent DNA damage sensor activity / response to ionizing radiation / translesion synthesis / ATP-dependent activity, acting on DNA / cell motility / single-stranded DNA binding ...DNA polymerase V complex / homologous recombination / recombinational repair / SOS response / ATP-dependent DNA damage sensor activity / response to ionizing radiation / translesion synthesis / ATP-dependent activity, acting on DNA / 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
Similarity search - Function
: / : / 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. ...: / : / 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. / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Protein RecA
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.3 Å
AuthorsPavletich, 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: Source and taxonomy / Category: entity_src_gen
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / 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_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: Protein recA
B: Protein recA
C: Protein recA
D: Protein recA
E: Protein recA
F: Protein recA
G: Protein recA
H: Protein recA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,176,51672
Polymers1,159,5408
Non-polymers16,97664
Water0
1
A: Protein recA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)147,0649
Polymers144,9421
Non-polymers2,1228
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Protein recA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)147,0649
Polymers144,9421
Non-polymers2,1228
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Protein recA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)147,0649
Polymers144,9421
Non-polymers2,1228
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Protein recA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)147,0649
Polymers144,9421
Non-polymers2,1228
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: Protein recA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)147,0649
Polymers144,9421
Non-polymers2,1228
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: Protein recA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)147,0649
Polymers144,9421
Non-polymers2,1228
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
7
G: Protein recA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)147,0649
Polymers144,9421
Non-polymers2,1228
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
8
H: Protein recA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)147,0649
Polymers144,9421
Non-polymers2,1228
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)176.600, 189.800, 424.300
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Protein recA / Recombinase A


Mass: 144942.438 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / References: UniProt: P0A7G6
#2: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 32 / Source method: obtained synthetically / Formula: Mg
#3: Chemical...
ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 32 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.07 Å3/Da / Density % sol: 59.89 %
Crystal growpH: 6.5
Details: RecA4 fusion protein mixed with 2 mM AMPPNP and 10 mM MgCl2, pH 7.5, followed by crystallization from 100 mM Bis-Tris-Cl, 7% (w/v) PEG 3350, 100 mM KSCN, 25% (v/v) ethylene glycol, pH 6.5.

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C
DetectorDate: Aug 1, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 4.3→40 Å / Num. obs: 87622

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Processing

SoftwareName: REFMAC / Version: 5.2.0019 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 4.3→20 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.92 / SU B: 150.646 / SU ML: 0.894 / Cross valid method: THROUGHOUT / ESU R Free: 1.051 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.26144 1810 2 %RANDOM
Rwork0.24314 ---
obs0.24351 87622 92.7 %-
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: 220.934 Å2
Baniso -1Baniso -2Baniso -3
1--5.04 Å20 Å20 Å2
2--5.79 Å20 Å2
3----0.75 Å2
Refinement stepCycle: LAST / Resolution: 4.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms70737 0 1024 0 71761
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.02272547
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6162.00297766
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.94259298
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.83125.2612853
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.6541513498
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.15415401
X-RAY DIFFRACTIONr_chiral_restr0.0980.211257
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0252278
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2530.230083
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3180.246554
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1680.22411
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0430.22
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.4870.2136
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2790.213
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9340.7547962
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.6761.2573260
X-RAY DIFFRACTIONr_scbond_it1.2351.2528570
X-RAY DIFFRACTIONr_scangle_it2.0962.2524506
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 4.301→4.407 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.356 107 -
Rwork0.371 5185 -
obs--77.36 %

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