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- PDB-2owy: The recombination-associated protein RdgC adopts a novel toroidal... -

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Basic information

Entry
Database: PDB / ID: 2owy
TitleThe recombination-associated protein RdgC adopts a novel toroidal architecture for DNA binding
ComponentsRecombination-associated protein rdgC
KeywordsDNA BINDING PROTEIN / homologous recombination / Pseudomonas aeruginosa / RdgC / RecA / ring-shaped DNA binding proteins
Function / homologyPutative exonuclease, RdgC / Putative exonuclease, RdgC / bacterial nucleoid / regulation of DNA recombination / double-stranded DNA binding / DNA recombination / cytoplasm / Recombination-associated protein RdgC
Function and homology information
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.5 Å
AuthorsSuh, S.W.
CitationJournal: Nucleic Acids Res. / Year: 2007
Title: The recombination-associated protein RdgC adopts a novel toroidal architecture for DNA binding
Authors: Ha, J.Y. / Kim, H.K. / Kim, D.J. / Kim, K.H. / Oh, S.J. / Lee, H.H. / Yoon, H.J. / Song, H.K. / Suh, S.W.
History
DepositionFeb 17, 2007Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 20, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Oct 18, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Recombination-associated protein rdgC
B: Recombination-associated protein rdgC


Theoretical massNumber of molelcules
Total (without water)68,1142
Polymers68,1142
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)87.494, 116.041, 76.028
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Recombination-associated protein rdgC


Mass: 34056.867 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: PAO1 / Gene: rdgC / Plasmid: pET21a(+) / Production host: Escherichia coli (E. coli) / Strain (production host): C41(DE3) / References: UniProt: Q9HYX7

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 3

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Sample preparation

CrystalDensity Matthews: 2.83 Å3/Da / Density % sol: 56.57 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M sodium HEPES (pH 7.5), 1.0M tri-sodium citrate, 1%(w/v) Anapoe 35, VAPOR DIFFUSION, HANGING DROP, temperature 297K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
31
1,21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONPhoton Factory AR-NW12A11.00000, 0.95000, 0.97913, 0.97897
SYNCHROTRONPAL/PLS 6B21.00000, 0.99188, 1.00875, 1.00842, 1.00637
Detector
TypeIDDetectorDateDetails
ADSC QUANTUM 2101CCDNov 23, 2005mirrors
BRUKER PROTEUM 3002CCDOct 12, 2005mirrors
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Numerical link type Si(111) double crystal monochromator, liquid nitrogen coolingMADMx-ray1
2Double Crystal MonochromatorMADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
111
20.951
30.979131
40.978971
50.991881
61.008751
71.008421
81.006371
Reflection

D res low: 30 Å

IDAv σ(I) over netINumberRmerge(I) obsΧ2D res high (Å)Num. obs% possible obs
116.41696160.0661.392.62442299.9
215.71679450.0721.52.62430499.9
314.31516880.0671.12.721864100
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squared
5.593099.310.0392.071
4.445.5910010.0471.918
3.884.4410010.0551.869
3.533.8810010.0671.682
3.283.5310010.081.458
3.083.2810010.1081.201
2.933.0810010.1471.028
2.82.9310010.1980.913
2.692.810010.280.926
2.62.6910010.3860.905
5.593099.320.0432.462
4.445.5910020.0512.189
3.884.4410020.0582.037
3.533.8810020.071.761
3.283.5310020.0841.538
3.083.2810020.1131.243
2.933.0810020.1551.05
2.82.9310020.2110.942
2.692.810020.2890.933
2.62.6910020.3990.889
5.83099.730.0351.557
4.615.810030.0471.456
4.034.6110030.0521.458
3.664.0310030.0651.216
3.43.6610030.0771.169
3.23.410030.1050.922
3.043.210030.1460.863
2.913.0410030.2060.777
2.82.9110030.2880.804
2.72.810030.4020.833
ReflectionResolution: 2.5→30 Å / Num. obs: 27126 / % possible obs: 100 % / Rmerge(I) obs: 0.054 / Χ2: 1.575 / Net I/σ(I): 21.9
Reflection shellResolution: 2.5→2.59 Å / Rmerge(I) obs: 0.279 / Num. unique all: 2663 / Χ2: 0.868 / % possible all: 99.9

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Phasing

PhasingMethod: MAD
Phasing set
ID
1
2
3
Phasing MADD res high: 2.7 Å / D res low: 30 Å / FOM : 0.49 / Reflection: 21062
Phasing MAD set
Clust-IDExpt-IDSet-IDWavelength (Å)F double prime refinedF prime refined
13 wavelength10.9794.48-7.52
13 wavelength20.97913.32-7.02
13 wavelength30.952.86-2.38
Phasing MAD set site
IDAtom type symbolB isoFract xFract yFract zOccupancy
1Se53.9760.3120.0710.030.999
2Se53.9760.7530.1790.4680.999
3Se40.8810.7060.2090.4330.999
4Se32.4380.7260.2040.4310.433
Phasing MAD shell
Resolution (Å)FOM Reflection
9.52-300.761124
6.08-9.520.81828
4.77-6.080.782291
4.05-4.770.712644
3.59-4.050.573013
3.25-3.590.393221
2.99-3.250.243409
2.79-2.990.143532
Phasing dmFOM : 0.58 / FOM acentric: 0.58 / FOM centric: 0.6 / Reflection: 21053 / Reflection acentric: 18545 / Reflection centric: 2508
Phasing dm shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
7.7-28.8990.930.950.89993699294
4.8-7.70.880.90.829532441512
3.9-4.80.840.850.7736253158467
3.4-3.90.680.690.5936153222393
2.9-3.40.390.40.3362005641559
2.7-2.90.190.20.1836673384283

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SOLVE2.03phasing
RESOLVE2.03phasing
CNSrefinement
PDB_EXTRACT2data extraction
ADSCQuantumdata collection
HKL-2000data reduction
RefinementMethod to determine structure: MAD / Resolution: 2.5→20 Å / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.279 2637 9.6 %
Rwork0.234 --
obs-26545 96.9 %
Solvent computationBsol: 38.622 Å2
Displacement parametersBiso mean: 48.198 Å2
Baniso -1Baniso -2Baniso -3
1--4.868 Å20 Å20 Å2
2--14.159 Å20 Å2
3----9.291 Å2
Refinement stepCycle: LAST / Resolution: 2.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4788 0 0 0 4788
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it1.4051.5
X-RAY DIFFRACTIONc_scbond_it1.9922
X-RAY DIFFRACTIONc_mcangle_it2.3742
X-RAY DIFFRACTIONc_scangle_it3.0432.5
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2water.param

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