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- PDB-2odn: MSRECA-dATP complex -

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Basic information

Entry
Database: PDB / ID: 2odn
TitleMSRECA-dATP complex
ComponentsProtein recA
KeywordsRECOMBINATION / DNA-REPAIR / SOS RESPONCE
Function / homology
Function and homology information


SOS response / ATP-dependent DNA damage sensor activity / single-stranded DNA binding / DNA recombination / damaged DNA binding / DNA repair / ATP binding / metal ion binding / cytoplasm
Similarity search - Function
RecA protein, C-terminal domain / Rec A Protein; domain 2 / 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 protein, C-terminal domain / Rec A Protein; domain 2 / 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
2'-DEOXYADENOSINE 5'-TRIPHOSPHATE / Protein RecA / Protein RecA
Similarity search - Component
Biological speciesMycobacterium smegmatis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsKrishna, R. / Rajan Prabu, J. / Manjunath, G.P. / Datta, S. / Chandra, N.R. / Muniyappa, K. / Vijayan, M.
Citation
Journal: J.Mol.Biol. / Year: 2007
Title: Snapshots of RecA protein involving movement of the C-domain and different conformations of the DNA-binding loops: crystallographic and comparative analysis of 11 structures of Mycobacterium smegmatis RecA
Authors: Krishna, R. / Prabu, J.R. / Manjunath, G.P. / Datta, S. / Chandra, N.R. / Muniyappa, K. / Vijayan, M.
#1: Journal: Nucleic Acids Res. / Year: 2000
Title: Crystal structures of Mycobacterium tuberculosis RecA and its complex with ADP-AlF(4): implications for decreased ATPase activity and molecular aggregation
Authors: Datta, S. / Prabu, M.M. / Vaze, M.B. / Ganesh, N. / Chandra, N.R. / Muniyappa, K. / Vijayan, M.
#2: Journal: Proteins / Year: 2003
Title: Structural studies on MtRecA-nucleotide complexes: insights into DNA and nucleotide binding and the structural signature of NTP recognition
Authors: Datta, S. / Ganesh, N. / Chandra, N.R. / Muniyappa, K. / Vijayan, M.
#3: Journal: J.Bacteriol. / Year: 2003
Title: Crystal structures of Mycobacterium smegmatis RecA and its nucleotide complexes
Authors: Datta, S. / Krishna, R. / Ganesh, N. / Chandra, N.R. / Muniyappa, K. / Vijayan, M.
#4: Journal: Nucleic Acids Res. / Year: 2006
Title: Crystallographic identification of an ordered C-terminal domain and a second nucleotide-binding site in RecA: new insights into allostery
Authors: Krishna, R. / Manjunath, G.P. / Kumar, P. / Surolia, A. / Chandra, N.R. / Muniyappa, K. / Vijayan, M.
History
DepositionDec 24, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 19, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 23, 2019Group: Data collection / Category: reflns / Item: _reflns.pdbx_Rmerge_I_obs

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein recA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,8362
Polymers37,3441
Non-polymers4911
Water54030
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)103.634, 103.634, 77.143
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

#1: Protein Protein recA / Recombinase A


Mass: 37344.488 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium smegmatis (bacteria) / Plasmid: PTHIOA / Production host: Escherichia coli (E. coli) / Strain (production host): JC10289
References: UniProt: Q59560, UniProt: Q7X416*PLUS, EC: 3.4.99.37
#2: Chemical ChemComp-DTP / 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE / Deoxyadenosine triphosphate


Mass: 491.182 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O12P3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 30 / 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: 3.2 Å3/Da / Density % sol: 61.58 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG 4000, CIT-PHOS, NACL, DTT, pH 7.50, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 25, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3.1→30 Å / Num. obs: 8634 / % possible obs: 99.6 % / Observed criterion σ(I): 0 / Redundancy: 5.3 % / Biso Wilson estimate: 44.5 Å2 / Rmerge(I) obs: 0.084 / Net I/σ(I): 6.1
Reflection shellResolution: 3.1→3.21 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 1.3 / % possible all: 99.5

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1UBC

1ubc


Resolution: 3.1→29.92 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 239092.09 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.285 825 10.6 %RANDOM
Rwork0.231 ---
obs0.231 7751 89.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 28.9737 Å2 / ksol: 0.215296 e/Å3
Displacement parametersBiso mean: 58.1 Å2
Baniso -1Baniso -2Baniso -3
1--10.37 Å20.49 Å20 Å2
2---10.37 Å20 Å2
3---20.74 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.53 Å0.43 Å
Luzzati d res low-5 Å
Luzzati sigma a1.04 Å0.85 Å
Refinement stepCycle: LAST / Resolution: 3.1→29.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2231 0 30 30 2291
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.7
X-RAY DIFFRACTIONc_dihedral_angle_d23.2
X-RAY DIFFRACTIONc_improper_angle_d0.98
X-RAY DIFFRACTIONc_mcbond_it11.561.5
X-RAY DIFFRACTIONc_mcangle_it17.942
X-RAY DIFFRACTIONc_scbond_it14.942
X-RAY DIFFRACTIONc_scangle_it20.372.5
LS refinement shellResolution: 3.1→3.29 Å / Rfactor Rfree error: 0.046 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.467 104 9 %
Rwork0.418 1050 -
obs--81 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dtp.paramdtp.top
X-RAY DIFFRACTION4water_rep.paramwater.top

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